icn3d 3.45.1 → 3.45.2

package/css/icn3d.css

@@ -1,31 +1,64 @@
+.ui-dialog { font-size: 12px;}
+.ui-dialog .ui-dialog-title { font-size: 16px; height: 18px; }
+.ui-dialog .ui-button { width: 12px; height:12px; margin: -5px 0px 0px 0px;}
+.ui-dialog .ui-dialog-titlebar { padding: 0px 1em 2px 1em; }
+
+.ui-dialog .ui-resizable-se {
+    width: 14px;
+    height: 14px;
+    right: 3px;
+    bottom: 3px;
+    background-position: -80px -224px;
+}
+
 /* theme: orange */
 /*
-.ui-widget-header{border:1px solid #e78f08;background:#f6a828 url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_35_f6a828_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
-.ui-button .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_ef8c08_256x240.png");}
-.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #eb8f00;text-decoration: none;}
+.icn3d-menu .ui-widget-header{border:1px solid #e78f08;background:#f6a828 url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_35_f6a828_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
+.icn3d-menu .ui-button .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_ef8c08_256x240.png");}
+.icn3d-menu .ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #eb8f00;text-decoration: none;}
 */
 
 /* theme: black */
 /*
-.ui-widget-header{border:1px solid #333333;background:#333333 url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_25_333333_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
-.ui-button .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_222222_256x240.png");}
-.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #222222;text-decoration: none;}
+.icn3d-menu .ui-widget-header{border:1px solid #333333;background:#333333 url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_25_333333_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
+.icn3d-menu .ui-button .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_222222_256x240.png");}
+.icn3d-menu .ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #222222;text-decoration: none;}
 */
 
 /* theme: blue */
-.ui-widget-header {border:1px solid #4297d7;background:#5c9ccc url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_55_5c9ccc_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
+.icn3d-menu .ui-widget-header {border:1px solid #4297d7;background:#5c9ccc url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_55_5c9ccc_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
 /*.ui-button .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_228ef1_256x240.png");}*/
-.ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_228ef1_256x240.png")!important;}
-.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #444;text-decoration: none;}
+.icn3d-menu .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_228ef1_256x240.png")!important;}
+.icn3d-menu .ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #444;text-decoration: none;}
 
-.icn3d-text {font-family: Verdana, Arial, Helvetica, sans-serif; font-size:12px!important;}
+.icn3d-menu .ui-accordion .ui-accordion-icons { padding-left: 0; text-align: center; }
 
-.ui-dialog { font-size: 12px;}
-.ui-dialog .ui-dialog-title { font-size: 16px; height: 18px; }
-.ui-dialog .ui-button { width: 12px; height:12px; margin: -5px 0px 0px 0px;}
-.ui-dialog .ui-dialog-titlebar { padding: 0px 1em 2px 1em; }
+.icn3d-menu .ui-menu-icon {
+    float: right;
+}
+
+.icn3d-menu .ui-widget {
+  font-family: Arial,Helvetica,sans-serif;
+  font-size: 12px!important; /* 0.9em is a little too large */
+}
+.icn3d-menu .ui-menu-item {
+  position: relative;
+  padding: 3px 1em 3px .4em;
+}
+
+/* remove the extra bar in the menu */
+    /* background: #eee url(images/ui-bg_highlight-soft_100_eeeeee_1x100.png) 50% top repeat-x; */
+.icn3d-menu .ui-widget-content {
+    border: 1px solid #ddd;
+    background: #eee;
+    color: #333;
+}
 
-.ui-accordion .ui-accordion-icons { padding-left: 0; text-align: center; }
+.icn3d-menu .ui-menu-icons .ui-menu-item-wrapper, .ui-menu-icons .ui-menu-item {
+    padding-left: 0.4em!important;
+}
+
+.icn3d-text {font-family: Verdana, Arial, Helvetica, sans-serif; font-size:12px!important;}
 
 .icn3d-menu {float:left; width:110px;}
 .icn3d-menu-color {color:#369; font-weight:bold; font-size: 14px!important;}
@@ -70,6 +103,7 @@ button, select, input { font-size: 10px; }
 
 .icn3d-dialog {font-family: Verdana, Arial, Helvetica, sans-serif; color: #666666;}
 .icn3d-commandTitle  {font-size: 12px; font-weight:bold; font-family: Verdana, Arial, Helvetica, sans-serif; color: #666666;}
+.icn3d-title  {font-size:1.2em; font-weight:normal; position:absolute; z-index:1; float:left; }
 .icn3d-modeselection  {color: #f8b84e!important;}
 /*.icn3d-viewselection  {color: #800000!important;}*/
 .icn3d-viewselection  {color: #f8b84e!important;}
@@ -98,18 +132,6 @@ button, select, input { font-size: 10px; }
 .icn3d-node-text24 {font-size: 24px; font-weight: bold}
 .icn3d-node-text32 {font-size: 32px; font-weight: bold}
 
-.ui-dialog .ui-resizable-se {
-    width: 14px;
-    height: 14px;
-    right: 3px;
-    bottom: 3px;
-    background-position: -80px -224px;
-}
-
-.ui-menu-icon {
-    float: right;
-}
-
 /* toggle button: http://www.w3schools.com/howto/howto_css_switch.asp */
 .icn3d-switch {
   position: relative;
@@ -178,15 +200,6 @@ input:checked + .icn3d-slider:before {
   overflow:auto;
 }
 
-.ui-widget {
-  font-family: Arial,Helvetica,sans-serif;
-  font-size: 12px!important; /* 0.9em is a little too large */
-}
-.ui-menu-item {
-  position: relative;
-  padding: 3px 1em 3px .4em;
-}
-
 .icn3d-clinvar {color:green; font-size:12px; font-weight:bold;}
 .icn3d-clinvar-path {color:red; font-size:12px; font-weight:bold;}
 
@@ -213,14 +226,6 @@ input:checked + .icn3d-slider:before {
 
 .icn3d-bkgd {background-color:#eee;}
 
-/* remove the extra bar in the menu */
-    /* background: #eee url(images/ui-bg_highlight-soft_100_eeeeee_1x100.png) 50% top repeat-x; */
-.ui-widget-content {
-    border: 1px solid #ddd;
-    background: #eee;
-    color: #333;
-}
-
 .icn3d-rad > input{ /* HIDE RADIO */
   visibility: hidden; /* Makes input not-clickable */
   position: absolute; /* Remove input from document flow */
@@ -240,10 +245,6 @@ input:checked + .icn3d-slider:before {
   background-position: -160px 0px; /*empty */
 }
 
-.ui-menu-icons .ui-menu-item-wrapper, .ui-menu-icons .ui-menu-item {
-    padding-left: 0.4em!important;
-}
-
 .icn3d-rad-text, .icn3d-color-rad-text {
     padding-left: 1.2em;
 }
@@ -288,7 +289,6 @@ input:checked + .icn3d-slider:before {
 
 .ncbi-page-header {
   background-color: #369;
-  color: #fff;
   overflow: auto;
 }
 

package/icn3d.js

@@ -58909,7 +58909,7 @@ class SetMenu {
         html += this.setTools();
 
         // show title at the top left corner
-        html += me.htmlCls.divStr + "title' class='icn3d-commandTitle' style='font-size:1.2em; font-weight:normal; position:absolute; z-index:1; float:left; display:table-row; margin: 85px 0px 0px 5px; color:" + titleColor + "; width:" + me.htmlCls.WIDTH + "px'></div>";
+        html += me.htmlCls.divStr + "title' class='icn3d-commandTitle icn3d-title' style='display:table-row; margin: 85px 0px 0px 5px; color:" + titleColor + "; width:" + me.htmlCls.WIDTH + "px'></div>";
 
         html += me.htmlCls.divStr + "viewer' style='position:relative; width:100%; height:100%; background-color: " + me.htmlCls.GREYD + ";'>";
 
@@ -59043,7 +59043,7 @@ class SetMenu {
         //html += me.htmlCls.setMenuCls.setTools();
 
         // show title at the top left corner
-        html += me.htmlCls.divStr + "title' class='icn3d-commandTitle' style='font-size:1.2em; font-weight:normal; position:absolute; z-index:1; float:left; display:block; margin: 12px 0px 0px 40px; color:" + titleColor + "; width:" +(me.htmlCls.WIDTH - 40).toString() + "px'></div>";
+        html += me.htmlCls.divStr + "title' class='icn3d-commandTitle icn3d-title' style='display:block; margin: 12px 0px 0px 40px; color:" + titleColor + "; width:" +(me.htmlCls.WIDTH - 40).toString() + "px'></div>";
         html += me.htmlCls.divStr + "viewer' style='position:relative; width:100%; height:100%; background-color: " + me.htmlCls.GREYD + ";'>";
         // don't show legend in mobile
         //html += me.htmlCls.divStr + "legend' class='icn3d-text icn3d-legend'></div>";
@@ -74243,7 +74243,7 @@ class Scene {
             ic.shininess = shininess;
         }
 
-        if(!me.bNode && me.htmlCls.setHtmlCls.getCookie('light1') != '') {
+        if(!me.bNode && me.htmlCls.setHtmlCls.getCookie('light1') != '' && !me.bNode && me.htmlCls.setHtmlCls.getCookie('light2') != '' && !me.bNode && me.htmlCls.setHtmlCls.getCookie('light3') != '') {
             let light1 = parseFloat(me.htmlCls.setHtmlCls.getCookie('light1'));
             let light2 = parseFloat(me.htmlCls.setHtmlCls.getCookie('light2'));
             let light3 = parseFloat(me.htmlCls.setHtmlCls.getCookie('light3'));
@@ -78993,19 +78993,25 @@ class Tube {
           //mesh = new THREE.Mesh(geo, new THREE.MeshPhongMaterial({ transparent: true, opacity: 0.5, specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, vertexColors: THREE.FaceColors, side: THREE.DoubleSide }));
           mesh = new Mesh$1(geo, new MeshPhongMaterial({ transparent: true, opacity: 0.5, specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, vertexColors: true, side: DoubleSide$1 }));
 
-          if(ic.mdl) ic.mdl.add(mesh);
+          if(ic.mdl) {
+            ic.mdl.add(mesh);
+          }
         }
         else if(bHighlight === 1) {
           mesh = new Mesh$1(geo, ic.matShader);
           mesh.renderOrder = ic.renderOrderPicking;
           //ic.mdlPicking.add(mesh);
-          if(ic.mdl) ic.mdl.add(mesh);
+          if(ic.mdl) {
+            ic.mdl.add(mesh);
+          }
         }
         else {
           //mesh = new THREE.Mesh(geo, new THREE.MeshPhongMaterial({ specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, vertexColors: THREE.FaceColors, side: THREE.DoubleSide }));
           mesh = new Mesh$1(geo, new MeshPhongMaterial({ specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, vertexColors: true, side: DoubleSide$1 }));
 
-          if(ic.mdl) ic.mdl.add(mesh);
+          if(ic.mdl) {
+            ic.mdl.add(mesh);
+          }
         }
 
         if(bHighlight === 1 || bHighlight === 2) {
@@ -83403,7 +83409,11 @@ class ApplyClbonds {
     applyClbondsOptions(options) { let ic = this.icn3d, me = ic.icn3dui;
        if(options === undefined) options = ic.opts;
 
-       if(!ic.bCalcCrossLink) {
+       ic.lines['clbond'] = [];
+
+       if(options.chemicals == 'nothing') return {};
+       
+    //    if(!ic.bCalcCrossLink) {
          // find all bonds to chemicals
          ic.clbondpnts = {};
          ic.clbondResid2serial = {};
@@ -83414,10 +83424,11 @@ class ApplyClbonds {
          // chemical to protein/nucleotide
          this.applyClbondsOptions_base('all');
 
-         ic.bCalcCrossLink = true;
-       }
+        //  ic.bCalcCrossLink = true;
+    //    }
 
-       if (options.clbonds.toLowerCase() === 'yes' && options.chemicals !== 'nothing') {
+    //    if (options.clbonds.toLowerCase() === 'yes' && options.chemicals !== 'nothing') {
+       if (options.clbonds.toLowerCase() === 'yes') {
          let color = '#006400';
          me.parasCls.thr(0x006400);
 
@@ -83443,7 +83454,8 @@ class ApplyClbonds {
                     line.serial1 = ic.clbondResid2serial[resid0 + ',' + resid1];
                     line.serial2 = ic.clbondResid2serial[resid1 + ',' + resid0];
 
-                    if(!ic.dAtoms.hasOwnProperty(line.serial1) || !ic.dAtoms.hasOwnProperty(line.serial2)) continue;
+                    // only apply to displayed atoms
+                    // if(!ic.dAtoms.hasOwnProperty(line.serial1) || !ic.dAtoms.hasOwnProperty(line.serial2)) continue;
 
                     line.position1 = ic.atoms[line.serial1].coord;
                     line.position2 = ic.atoms[line.serial2].coord;
@@ -83475,9 +83487,14 @@ class ApplyClbonds {
       return ic.residuesHashClbonds;
     }
 
-    applyClbondsOptions_base(type) { let ic = this.icn3d; ic.icn3dui;
+    applyClbondsOptions_base(type) { let ic = this.icn3d, me = ic.icn3dui;
+         // only apply to displayed atoms
+         let atomHash = me.hashUtilsCls.cloneHash(ic.chemicals);
+         atomHash = me.hashUtilsCls.intHash(atomHash, ic.dAtoms);
+
          // chemical to chemical first
-         for (let i in ic.chemicals) {
+        //   for (let i in ic.chemicals) {
+         for (let i in atomHash) {
             let atom0 = ic.atoms[i];
 
             let chain0 = atom0.structure + '_' + atom0.chain;
@@ -86072,24 +86089,27 @@ class Instancing {
            let normalArray2 = (baseGeometry.attributes.normal) ? me.hashUtilsCls.hashvalue2array(baseGeometry.attributes.normal.array) : [];
            let colorArray2 = (baseGeometry.attributes.color) ? me.hashUtilsCls.hashvalue2array(baseGeometry.attributes.color.array) : [];
            let indexArray2 = (baseGeometry.index) ? me.hashUtilsCls.hashvalue2array(baseGeometry.index.array) : [];
+          
+           if(colorArray2.length > 0) { // avoid an black object in the center of of assembly, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/?pdbid=1qqp
+                positionArray = positionArray.concat(positionArray2);
+                normalArray = normalArray.concat(normalArray2);
+                colorArray = colorArray.concat(colorArray2);
+                indexArray = indexArray.concat(indexArray2);
 
-           positionArray = positionArray.concat(positionArray2);
-           normalArray = normalArray.concat(normalArray2);
-           colorArray = colorArray.concat(colorArray2);
-           indexArray = indexArray.concat(indexArray2);
-
-           let bCylinderArray = [];
-           let bCylinder = (baseGeometry.type == 'CylinderGeometry') ? 1.0 : 0.0;
-           for(let i = 0, il = positionArray.length / 3; i < il; ++i) {
-               bCylinderArray.push(bCylinder);
-           }
+                let bCylinderArray = [];
+                let bCylinder = (baseGeometry.type == 'CylinderGeometry') ? 1.0 : 0.0;
+                //    let bCylinder = (baseGeometry.geometry.type == 'CylinderGeometry') ? 1.0 : 0.0;
+                for(let i = 0, il = positionArray.length / 3; i < il; ++i) {
+                    bCylinderArray.push(bCylinder);
+                }
 
-           geometry.setAttribute('position', new BufferAttribute$1(new Float32Array(positionArray), 3));
-           geometry.setAttribute('normal', new BufferAttribute$1(new Float32Array(normalArray), 3) );
-           geometry.setAttribute('color', new BufferAttribute$1(new Float32Array(colorArray), 3) );
+                geometry.setAttribute('position', new BufferAttribute$1(new Float32Array(positionArray), 3));
+                geometry.setAttribute('normal', new BufferAttribute$1(new Float32Array(normalArray), 3) );
+                geometry.setAttribute('color', new BufferAttribute$1(new Float32Array(colorArray), 3) );
 
-           geometry.setAttribute('cylinder', new BufferAttribute$1(new Float32Array(bCylinderArray), 1) );
-           geometry.setIndex(new BufferAttribute$1(new Uint32Array(indexArray), 1));
+                geometry.setAttribute('cylinder', new BufferAttribute$1(new Float32Array(bCylinderArray), 1) );
+                geometry.setIndex(new BufferAttribute$1(new Uint32Array(indexArray), 1));
+           }
 
            positionArray2 = null;
            normalArray2 = null;
@@ -86151,7 +86171,7 @@ class Instancing {
 
            let mesh2 = new Mesh$1(geometry, ic.instancedMaterial);
 
-           mesh2.onBeforeRender = ic.impostorCls.onBeforeRender;
+           if(ic.bImpo) mesh2.onBeforeRender = ic.impostorCls.onBeforeRender;
            //mesh2.onBeforeRender = this.onBeforeRender;
 
            // important: https://stackoverflow.com/questions/21184061/mesh-suddenly-disappears-in-three-js-clipping
@@ -86377,7 +86397,7 @@ class Alternate {
 
         //ic.glycanCls.showGlycans();
 
-        ic.opts['rotationcenter'] = 'highlight center';
+        // ic.opts['rotationcenter'] = 'highlight center';
         
         ic.drawCls.draw();
 
@@ -96628,9 +96648,14 @@ class Annotation {
         $("[id^=" + ic.pre + "transmem]").hide();
         if($("#" + ic.pre + "anno_transmem").length) $("#" + ic.pre + "anno_transmem")[0].checked = false;
     }
-    async setAnnoTabIg(bSelection, template) {  let ic = this.icn3d; ic.icn3dui;
+    async setAnnoTabIg(bSelection, template) {  let ic = this.icn3d, me = ic.icn3dui;
+        let selAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
+
         await this.updateIg(bSelection, template);
 
+        // preserve previous selection
+        ic.hAtoms = me.hashUtilsCls.cloneHash(selAtoms);
+
         $("[id^=" + ic.pre + "ig]").show();
         if($("#" + ic.pre + "anno_ig").length) $("#" + ic.pre + "anno_ig")[0].checked = true;
     }