Merge pull request #137 in STRUC/icn3d from release279 to master

* commit '2e8b910791d69bd81ddbdd8b38f68a8b8933555c':
  Fixed the effect of Fog on sticks and spheres

CHANGELOG.md

@@ -1,4 +1,6 @@
 ## Change Log
+[icn3d-2.7.9](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.7.9.zip) was release on August 1, 2019. Fixed the effect of Fog on sticks and spheres.
+
 [icn3d-2.7.8](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.7.8.zip) was release on July 31, 2019. Fixed SNP annotation in the sequences and annotations window.
 
 [icn3d-2.7.7](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.7.7.zip) was release on July 30, 2019. Added the option to show or hide hydrogens when displaying PubChem compounds.

README.md

@@ -21,7 +21,7 @@ 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 as shown in the section of "Embed iCn3D with iframe or JavaScript libraries" below. 
 
-<b>Complete package</b> of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.7.8.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.7.8.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-2.7.9.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.7.9.zip). The "Download ZIP" link in this page does not include third-party libraries. 
 
 ## [Gallery](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#gallery)
 

icn3d.html

@@ -508,8 +508,14 @@ <h2>iCn3D gallery <span style="font-size:0.7em">("iCn3D PNG Images", all images
 </div>
 
 <div class="gallery">
-<a href="https://icn3d.page.link/aRyqxdcTWuUfJcYE6" target="_blank">
-<img style="height:300px" src ="https://www.ncbi.nlm.nih.gov/Structure/icn3d/gallery/3GVU-aRyqxdcTWuUfJcYE6.png"><br>Ligand Binding (PDB 3GVU)
+<a href="https://icn3d.page.link/WTtKKEaYkeMRE5nP7" target="_blank">
+<img style="height:300px" src ="https://www.ncbi.nlm.nih.gov/Structure/icn3d/gallery/3GVU-b1-WTtKKEaYkeMRE5nP7"><br>Ligand Binding with Fog (PDB 3GVU)
+</a>
+</div>
+
+<div class="gallery">
+<a href="https://icn3d.page.link/4ZXgp2mSnXT8vbqf7" target="_blank">
+<img style="height:300px" src ="https://www.ncbi.nlm.nih.gov/Structure/icn3d/gallery/3GVU-b2-4ZXgp2mSnXT8vbqf7.png"><br>Ligand Binding with Labels (PDB 3GVU)
 </a>
 </div>
 
@@ -1940,6 +1946,9 @@ <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-2.7.9.zip">icn3d-2.7.9</a> was release on August 1, 2019. Fixed the effect of Fog on sticks and spheres.
+<br><br>
+
 <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.7.8.zip">icn3d-2.7.8</a> was release on July 31, 2019. Fixed SNP annotation in the sequences and annotations window.
 <br><br>
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "2.7.8",
+  "version": "2.7.9",
   "description": "iCn3D Structure Viewer",
   "main": "index.html",
   "scripts": {

src/icn3d/draw/impostor.js

@@ -201,6 +201,7 @@ iCn3D.prototype.setParametersForShader = function (opacity) { var me = this;
 
     if(this.opts['fog'] === 'yes') {
         this.defines['USE_FOG'] = 1;
+
         if(this.opts['camera'] === 'orthographic') {
             this.defines['FOG_EXP2'] = 1;
         }

src/icn3dui/full_ui.js

@@ -15,7 +15,7 @@ if (!$.ui.dialog.prototype._makeDraggableBase) {
 var iCn3DUI = function(cfg) {
     var me = this;
 
-    this.REVISION = '2.7.8';
+    this.REVISION = '2.7.9';
 
     me.bFullUi = true;
 

src/icn3dui/selection/commands.js

@@ -1095,7 +1095,7 @@ iCn3DUI.prototype.applyCommand = function (commandStr) { var me = this;
     var radius = parseFloat(paraArray[0].substr(paraArray[0].lastIndexOf(' ') + 1));
 
     var nameArray = [];
-    if(paraArray.length == 2) {
+    if(paraArray.length == 2 && paraArray[1].length > 4) { //sets a,b,c
         var nameStr = paraArray[1].substr(paraArray[1].indexOf(' ') + 1);
         nameArray = nameStr.split(",");
     }
@@ -1292,7 +1292,7 @@ iCn3DUI.prototype.applyCommand = function (commandStr) { var me = this;
 
     var threshold = parseFloat(paraArray[0].substr(paraArray[0].indexOf(' ') + 1));
     var nameArray = [];
-    if(paraArray.length == 2) {
+    if(paraArray.length == 2 && paraArray[1].length > 4) { //sets a,b,c
         var nameStr = paraArray[1].substr(paraArray[1].indexOf(' ') + 1);
         nameArray = nameStr.split(",");
     }

src/shader/CylinderImpostor.frag

@@ -294,7 +294,21 @@ $NGL_shaderTextHash['CylinderImpostor.frag'] = ["#define STANDARD",
 "        #include premultiplied_alpha_fragment",
 "        #include tonemapping_fragment",
 "        #include encodings_fragment",
-"        #include fog_fragment",
+"        //include fog_fragment",
+"        #ifdef USE_FOG",
+"            #ifdef USE_LOGDEPTHBUF_EXT",
+"                float depth = gl_FragDepthEXT / gl_FragCoord.w;",
+"            #else",
+"                float depth = gl_FragCoord.z / gl_FragCoord.w;",
+"            #endif",
+"            #ifdef FOG_EXP2",
+"                float fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );",
+"            #else",
+"                float fogFactor = smoothstep( fogNear, fogFar, depth );",
+"            #endif",
+"            gl_FragColor.rgb = mix( gl_FragColor.rgb, fogColor, fogFactor );",
+"        #endif",
+"",
 "    #endif",
 "",
 "}"

src/shader/CylinderImpostor.vert

@@ -37,6 +37,8 @@ $NGL_shaderTextHash['CylinderImpostor.vert'] = ["// Open-Source PyMOL is Copyrig
 "varying vec3 V;",
 "varying vec4 w;",
 "varying float fogDepth;",
+"varying float fogNear;",
+"varying float fogFar;",
 "",
 "#ifdef PICKING",
 "    #include unpack_clr",

src/shader/CylinderInstancing.vert

@@ -41,6 +41,8 @@ $NGL_shaderTextHash['CylinderInstancing.vert'] = ["// Open-Source PyMOL is Copyr
 "varying vec3 V;",
 "varying vec4 w;",
 "varying float fogDepth;",
+"varying float fogNear;",
+"varying float fogFar;",
 "",
 "#ifdef PICKING",
 "    #include unpack_clr",

src/shader/SphereImpostor.frag

@@ -162,7 +162,20 @@ $NGL_shaderTextHash['SphereImpostor.frag'] = ["#define STANDARD",
 "        #include premultiplied_alpha_fragment",
 "        #include tonemapping_fragment",
 "        #include encodings_fragment",
-"        #include fog_fragment",
+"        //include fog_fragment",
+"        #ifdef USE_FOG",
+"            #ifdef USE_LOGDEPTHBUF_EXT",
+"                float depth = gl_FragDepthEXT / gl_FragCoord.w;",
+"            #else",
+"                float depth = gl_FragCoord.z / gl_FragCoord.w;",
+"            #endif",
+"            #ifdef FOG_EXP2",
+"                float fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );",
+"            #else",
+"                float fogFactor = smoothstep( fogNear, fogFar, depth );",
+"            #endif",
+"            gl_FragColor.rgb = mix( gl_FragColor.rgb, fogColor, fogFactor );",
+"        #endif",
 "",
 "    #endif",
 "",

src/shader/SphereImpostor.vert

@@ -6,6 +6,8 @@ $NGL_shaderTextHash['SphereImpostor.vert'] = ["uniform mat4 projectionMatrixInve
 "varying vec3 vPoint;",
 "varying vec3 vPointViewPosition;",
 "varying float fogDepth;",
+"varying float fogNear;",
+"varying float fogFar;",
 "",
 "attribute vec2 mapping;",
 "//attribute vec3 position;",

src/shader/SphereInstancing.vert

@@ -6,6 +6,8 @@ $NGL_shaderTextHash['SphereInstancing.vert'] = ["uniform mat4 projectionMatrixIn
 "varying vec3 vPoint;",
 "varying vec3 vPointViewPosition;",
 "varying float fogDepth;",
+"varying float fogNear;",
+"varying float fogFar;",
 "",
 "attribute vec2 mapping;",
 "//attribute vec3 position;",