Merge pull request #60 in STRUC/icn3d from release214 to master

* commit '6a9c55fd9d9ebc352976893f666710c78b8300be':
  The retrieval of transformation matrix from mmCIF was fixed for Mac

README.md

@@ -19,7 +19,7 @@ We provided two types of iCn3D widgets: [basic interface](https://www.ncbi.nlm.n
 
 Either of these widgets could be easily added to your own web pages. Please see the [help page](https://www.ncbi.nlm.nih.gov/Structure/icn3d/docs/icn3d_help.html#HowToUse) for more details.
 
-<b>Complete package</b> of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.1.3.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.1.3.zip). The "Download ZIP" link in this page does not include third-party libraries. 
+<b>Complete package</b> of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.1.4.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.1.4.zip). The "Download ZIP" link in this page does not include third-party libraries. 
 
 ## Usage
 
@@ -77,6 +77,8 @@ gulp
 ```
 
 ## Change log
+The production version [icn3d-2.1.4](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.1.4.zip) was release on June 7, 2018. The retrieval of transformation matrix from mmCIF was fixed for Mac.
+
 The production version [icn3d-2.1.3](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.1.3.zip) was release on May 30, 2018.  "Sequences and Annotations" is now able to be highlighted even if some annotations didn't show up.
 
 The production version [icn3d-2.1.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.1.2.zip) was release on May 23, 2018. The surface display was improved by adding light reflection. Light was added to the display of instanced biological assemblies.

icn3d.html

@@ -1700,6 +1700,9 @@ <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>
+The production version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.1.4.zip">icn3d-2.1.4</a> was release on June 7, 2018. The retrieval of transformation matrix from mmCIF was fixed for Mac.
+<br><br>
+
 The production version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.1.3.zip">icn3d-2.1.3</a> was release on May 30, 2018.  "Sequences and Annotations" is now able to be highlighted even if some annotations didn't show up.
 <br><br>
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "2.1.3",
+  "version": "2.1.4",
   "description": "iCn3D Structure Viewer",
   "main": "index.html",
   "scripts": {

src/icn3dui/full_ui.js

@@ -614,11 +614,6 @@ iCn3DUI.prototype = {
       // display the structure right away. load the mns and sequences later
       setTimeout(function(){
           if(me.bInitial) {
-              if(me.cfg.showanno !== undefined && me.cfg.showanno) {
-                   me.showAnnotations();
-                   me.setLogCmd("view annotations", true);
-              }
-
               if(me.cfg.showsets !== undefined && me.cfg.showsets) {
                    me.showSets();
               }
@@ -632,6 +627,23 @@ iCn3DUI.prototype = {
               }
 
               //me.setProtNuclLigInMenu();
+
+              if(me.cfg.showanno !== undefined && me.cfg.showanno) {
+                   var cmd = "view annotations";
+                   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);
+                   }
+*/
+              }
           }
           else {
               me.updateHlAll();

src/icn3dui/parsers/mmcif_mmdb_parser.js

@@ -92,7 +92,12 @@ iCn3DUI.prototype.downloadMmcifSymmetry = function (mmcifid) { var me = this;
 iCn3DUI.prototype.downloadMmcifSymmetryBase = function (mmcifid) { var me = this;
    var url, dataType;
 
-   url = "https://files.rcsb.org/header/" + mmcifid + ".cif";
+   if(me.isMac()) { // safari has a problem in getting data from https://files.rcsb.org/header/
+       url = "https://files.rcsb.org/view/" + mmcifid + ".cif";
+   }
+   else {
+       url = "https://files.rcsb.org/header/" + mmcifid + ".cif";
+   }
 
    dataType = "text";
 
@@ -193,46 +198,16 @@ iCn3DUI.prototype.loadMmcifData = function(data) { var me = this;
 };
 
 iCn3DUI.prototype.loadMmcifSymmetry = function(data) { var me = this;
-    //if(me.cfg.align === undefined && Object.keys(me.icn3d.structures).length == 1) {
-    //    $("#" + me.pre + "alternateWrapper").hide();
-    //}
-
     // load assembly info
     var assembly = data.assembly;
     var pmatrix = data.pmatrix;
 
-//    var pmatrixMat4 = new THREE.Matrix4();
-//    pmatrixMat4.fromArray(pmatrix);
-
-//console.log("pmatrix: " + JSON.stringify(pmatrix));
-
     for(var i = 0, il = assembly.length; i < il; ++i) {
-//console.log("i: " + i + " matrix1: " + JSON.stringify(assembly[i]));
-
-      //var pmatrixInverseMat4 = new THREE.Matrix4();
-      //pmatrixInverseMat4.getInverse(pmatrixMat4);
-
       var mat4 = new THREE.Matrix4();
       mat4.fromArray(assembly[i]);
 
-      //pmatrixInverseMat4.multiply(mat4).multiply(pmatrixMat4);
-//      mat4.multiplyMatrices(pmatrixMat4, mat4);
-
-//console.log("mat4.elements: " + JSON.stringify(mat4.elements));
-
-/*
-      if (me.icn3d.biomtMatrices[i] == undefined) me.icn3d.biomtMatrices[i] = new THREE.Matrix4().identity();
-
-      for(var j = 0, jl = assembly[i].length; j < jl; ++j) {
-        //me.icn3d.biomtMatrices[i].elements[j] = assembly[i][j];
-        //me.icn3d.biomtMatrices[i].elements[j] = pmatrixInverseMat4.elements[j];
-        me.icn3d.biomtMatrices[i].elements[j] = mat4.elements[j];
-      }
-*/
-
       me.icn3d.biomtMatrices[i] = mat4;
     }
-//console.log("me.icn3d.biomtMatrices: " + JSON.stringify(me.icn3d.biomtMatrices));
 
     me.icn3d.asuCnt = me.icn3d.biomtMatrices.length;
 };
@@ -435,6 +410,11 @@ iCn3DUI.prototype.getMissingResidues = function (seqArray, type, chainid) { var
             resiPos = 1;
         }
 
+        // fixe some missing residue names such as residue 6 in 5C1M_A
+        if(seqName === '') {
+            seqName = 'x';
+        }
+
         var resObject = {};
         resObject.resi = i + 1;
         var resi = parseInt(seqArray[i][resiPos]);
@@ -597,7 +577,6 @@ iCn3DUI.prototype.loadAtomDataIn = function (data, id, type, seqalign) { var me
         }
     }
 
-
     var atomid2serial = {};
     var prevStructureNum = '', prevChainNum = '', prevResidueNum = '';
     var structureNum = '', chainNum = '', residueNum = '';
@@ -881,14 +860,13 @@ iCn3DUI.prototype.loadAtomDataIn = function (data, id, type, seqalign) { var me
           }
 
           // me.icn3d.chainsSeq[chainid][atm.resi - 1] should have been defined for major chains
-          if( (type === 'mmdbid' || type === 'mmcifid')  && bChainSeqSet && me.icn3d.chainsSeq[chainid][atm.resi - 1] !== undefined) {
+          if( bChainSeqSet && me.icn3d.chainsSeq[chainid][atm.resi - 1] !== undefined) {
               me.icn3d.chainsSeq[chainid][atm.resi - 1].name = oneLetterRes;
           }
-          else {
+          else if(!bChainSeqSet) {
               var resObject = {};
               resObject.resi = atm.resi;
               resObject.name = oneLetterRes;
-
               var numberStr = '';
               if(atm.resi % 10 === 0) numberStr = atm.resi.toString();