icn3d 3.45.0 → 3.45.2

package/icn3d.module.js

@@ -59810,7 +59810,7 @@ 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 + ";'>";
 
@@ -59944,7 +59944,7 @@ 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>";
@@ -75144,7 +75144,7 @@ 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'));
@@ -79894,19 +79894,25 @@ 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) {
@@ -84304,7 +84310,11 @@ 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 = {};
@@ -84315,10 +84325,11 @@ 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);
 
@@ -84344,7 +84355,8 @@ 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;
@@ -84376,9 +84388,14 @@ 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;
@@ -86973,24 +86990,27 @@ 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;
@@ -87052,7 +87072,7 @@ 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
@@ -87278,7 +87298,7 @@ class Alternate {
 
         //ic.glycanCls.showGlycans();
 
-        ic.opts['rotationcenter'] = 'highlight center';
+        // ic.opts['rotationcenter'] = 'highlight center';
         
         ic.drawCls.draw();
 
@@ -97529,9 +97549,14 @@ 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;
     }
@@ -128949,7 +128974,6 @@ class Transform {
                 ic.quaternion._y = transformation.quaternion._y;
                 ic.quaternion._z = transformation.quaternion._z;
                 ic.quaternion._w = transformation.quaternion._w;
-                bSet1 = true;
             }
             else { // |||pos:a,b,c|dir:a,b,c|up:a,b,c|fov:a
                 let bcfArray = commandTransformation[1].split('|');
@@ -128971,8 +128995,6 @@ class Transform {
                         }
                     }
                 });
-
-
             }
         }
         else {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "3.45.0",
+  "version": "3.45.2",
   "main": "./icn3d.js",
   "exports": {
     ".": {