icn3d 3.44.3 → 3.45.0

package/icn3d.js

@@ -55114,7 +55114,7 @@ class MyEventCls {
     }
 
     onId(id, eventName, myFunction) { this.icn3dui;
-        if(Object.keys(window).length < 2) return;
+        if(Object.keys(window).length < 3) return;
 
         if(id.substr(0, 1) == '#') id = id.substr(1);
         if(document.getElementById(id)) {
@@ -74147,13 +74147,18 @@ class Scene {
     rebuildScene(options) { let ic = this.icn3d, me = ic.icn3dui;
         if(options === undefined) options = ic.opts;
 
+        // whether camera was set
+        me.bCamera = (ic.cam) ? true : false;
+
         this.rebuildSceneBase(options);
 
         ic.fogCls.setFog();
 
-        // if(!ic.bVr && !ic.bAr) { // first time
+        if(ic.bSetCamera) { // load a URL with trackball transformation, or no info after "|||"
             ic.cameraCls.setCamera();
-        // }
+        }
+
+        if(ic.opts['slab'] === 'yes') ic.cameraCls.setSlab();
 
         // if(!ic.bSetVrArButtons) { // call once
         if(!me.cfg.imageonly) this.setVrArButtons();
@@ -75353,7 +75358,7 @@ function TrackballControls( object, domElement, icn3d ) {
     function keydown( event ) {
 //console.log("keydown");
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         window.removeEventListener( 'keydown', keydown );
 
@@ -75384,7 +75389,7 @@ function TrackballControls( object, domElement, icn3d ) {
     function keyup( event ) {
 //console.log("keyup");
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         _this._state = _prevState;
 
@@ -75394,7 +75399,7 @@ function TrackballControls( object, domElement, icn3d ) {
 
     function mousedown( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         //event.preventDefault();
         event.stopPropagation();
@@ -75431,7 +75436,7 @@ function TrackballControls( object, domElement, icn3d ) {
 
     function mousemove( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         //event.preventDefault();
         event.stopPropagation();
@@ -75454,7 +75459,7 @@ function TrackballControls( object, domElement, icn3d ) {
     }
 
     function mouseup( event ) {
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         //event.preventDefault();
         event.stopPropagation();
@@ -75469,7 +75474,7 @@ function TrackballControls( object, domElement, icn3d ) {
 
     function mousewheel( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         //event.preventDefault();
         event.stopPropagation();
@@ -75496,7 +75501,7 @@ function TrackballControls( object, domElement, icn3d ) {
 
     function touchstart( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         switch ( event.touches.length ) {
             case 1:
@@ -75528,7 +75533,7 @@ function TrackballControls( object, domElement, icn3d ) {
 
     function touchmove( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         //event.preventDefault();
         event.stopPropagation();
@@ -75558,7 +75563,7 @@ function TrackballControls( object, domElement, icn3d ) {
 
     function touchend( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         switch ( event.touches.length ) {
 
@@ -75583,7 +75588,7 @@ function TrackballControls( object, domElement, icn3d ) {
 
     }
 
-    if(Object.keys(window).length >= 2 && this.domElement) {
+    if(Object.keys(window).length >= 3 && this.domElement) {
         this.domElement.addEventListener( 'contextmn', function ( event ) {
             //event.preventDefault();
         }, false );
@@ -75597,8 +75602,8 @@ function TrackballControls( object, domElement, icn3d ) {
         this.domElement.addEventListener( 'touchend', touchend, false );
         this.domElement.addEventListener( 'touchmove', touchmove, false );
 
-        if(Object.keys(window).length >= 2) window.addEventListener( 'keydown', keydown, false );
-        if(Object.keys(window).length >= 2) window.addEventListener( 'keyup', keyup, false );
+        if(Object.keys(window).length >= 3) window.addEventListener( 'keydown', keydown, false );
+        if(Object.keys(window).length >= 3) window.addEventListener( 'keyup', keyup, false );
     }
 
     this.handleResize();
@@ -76031,7 +76036,7 @@ function OrthographicTrackballControls( object, domElement, icn3d ) { var me = t
 
     function keydown( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         window.removeEventListener( 'keydown', keydown );
 
@@ -76059,7 +76064,7 @@ function OrthographicTrackballControls( object, domElement, icn3d ) { var me = t
 
     function keyup( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         _this._state = _prevState;
 
@@ -76069,7 +76074,7 @@ function OrthographicTrackballControls( object, domElement, icn3d ) { var me = t
 
     function mousedown( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         //event.preventDefault();
         event.stopPropagation();
@@ -76106,7 +76111,7 @@ function OrthographicTrackballControls( object, domElement, icn3d ) { var me = t
 
     function mousemove( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         //event.preventDefault();
         event.stopPropagation();
@@ -76129,7 +76134,7 @@ function OrthographicTrackballControls( object, domElement, icn3d ) { var me = t
 
     function mouseup( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         //event.preventDefault();
         event.stopPropagation();
@@ -76144,7 +76149,7 @@ function OrthographicTrackballControls( object, domElement, icn3d ) { var me = t
 
     function mousewheel( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         //event.preventDefault();
         event.stopPropagation();
@@ -76170,7 +76175,7 @@ function OrthographicTrackballControls( object, domElement, icn3d ) { var me = t
 
     function touchstart( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         switch ( event.touches.length ) {
 
@@ -76203,7 +76208,7 @@ function OrthographicTrackballControls( object, domElement, icn3d ) { var me = t
 
     function touchmove( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         //event.preventDefault();
         event.stopPropagation();
@@ -76233,7 +76238,7 @@ function OrthographicTrackballControls( object, domElement, icn3d ) { var me = t
 
     function touchend( event ) {
 
-        if ( _this.enabled === false || Object.keys(window).length < 2)  return;
+        if ( _this.enabled === false || Object.keys(window).length < 3)  return;
 
         switch ( event.touches.length ) {
 
@@ -76258,7 +76263,7 @@ function OrthographicTrackballControls( object, domElement, icn3d ) { var me = t
 
     }
 
-    if(Object.keys(window).length >= 2 && this.domElement) {
+    if(Object.keys(window).length >= 3 && this.domElement) {
         this.domElement.addEventListener( 'contextmn', function ( event ) {
             //event.preventDefault();
         }, false );
@@ -76304,7 +76309,8 @@ class Camera {
 
             let maxD = ic.maxD;
 
-            if(window.cam === ic.perspectiveCamera) {
+            // if(window.cam === ic.perspectiveCamera) {
+            if(ic.opts.camera.toLowerCase() == 'perspective') {
                 let bInstance = (ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > ic.maxatomcnt) ? true : false;
                 //var factor = (ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > 10 * ic.maxatomcnt) ? 1 : 2;
                 //var factor = (ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > 10 * ic.maxatomcnt) ? 1 : 3;
@@ -76319,26 +76325,26 @@ class Camera {
                 }
 
                 if(window.cam_z > 0) {
-                  window.cam.position.z = maxD * window.camMaxDFactor; // for perspective, the z position should be large enough to see the whole molecule
+                    window.cam.position.z = maxD * window.camMaxDFactor; // for perspective, the z position should be large enough to see the whole molecule
                 }
                 else {
-                  window.cam.position.z = -maxD * window.camMaxDFactor; // for perspective, the z position should be large enough to see the whole molecule
+                    window.cam.position.z = -maxD * window.camMaxDFactor; // for perspective, the z position should be large enough to see the whole molecule
                 }
 
-                if(ic.opts['slab'] === 'yes') {
-                    if(bInstance) {
-                        window.cam.near = 0.1;
-                    }
-                    else if(window.camMaxDFactorFog !== undefined) {
-                        window.cam.near = maxD * window.camMaxDFactorFog - 10; // keep some surrounding residues
-                    }
-                    else {
-                        window.cam.near = maxD * window.camMaxDFactor;
-                    }
-                }
-                else {
+                // if(ic.opts['slab'] === 'yes') {
+                //     if(bInstance) {
+                //         window.cam.near = 0.1;
+                //     }
+                //     else if(window.camMaxDFactorFog !== undefined) {
+                //         window.cam.near = maxD * window.camMaxDFactorFog - 10; // keep some surrounding residues
+                //     }
+                //     else {
+                //         window.cam.near = maxD * window.camMaxDFactor;
+                //     }
+                // }
+                // else {
                     window.cam.near = 0.1;
-                }
+                // }
                 window.cam.far = 10000;
 
                 if(ic.bControlGl && !me.bNode) {
@@ -76353,7 +76359,8 @@ class Camera {
                     }
                 }
             }
-            else if (window.cam === ic.orthographicCamera){
+            // else if (window.cam === ic.orthographicCamera){
+            else if(ic.opts.camera.toLowerCase() == 'orthographic') {
                 if(ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > 10 * ic.maxatomcnt) {
                     window.cam.right = ic.maxD/2 * 1.5;
                 }
@@ -76365,12 +76372,12 @@ class Camera {
                 window.cam.top = window.cam.right /ic.container.whratio;
                 window.cam.bottom = -window.cam.right /ic.container.whratio;
 
-                  if(ic.opts['slab'] === 'yes') {
-                      window.cam.near = ic.maxD * 2;
-                  }
-                  else {
+                //   if(ic.opts['slab'] === 'yes') {
+                //       window.cam.near = ic.maxD * 2;
+                //   }
+                //   else {
                     window.cam.near = 0;
-                  }
+                //   }
 
                   window.cam.far = 10000;
 
@@ -76396,7 +76403,8 @@ class Camera {
 
             let maxD = ic.maxD;
 
-            if(ic.cam === ic.perspectiveCamera) {
+            // if(ic.cam === ic.perspectiveCamera) {
+            if(ic.opts.camera.toLowerCase() == 'perspective') {
                 let bInstance = (ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > ic.maxatomcnt) ? true : false;
                 //var factor = (ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > 10 * ic.maxatomcnt) ? 1 : 2;
                 //var factor = (ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > 10 * ic.maxatomcnt) ? 1 : 3;
@@ -76411,26 +76419,26 @@ class Camera {
                 }
 
                 if(ic.cam_z > 0) {
-                  ic.cam.position.z = maxD * ic.camMaxDFactor; // forperspective, the z positionshould be large enough to see the whole molecule
+                    ic.cam.position.z = maxD * ic.camMaxDFactor; // forperspective, the z positionshould be large enough to see the whole molecule
                 }
                 else {
-                  ic.cam.position.z = -maxD * ic.camMaxDFactor; // forperspective, the z positionshould be large enough to see the whole molecule
+                    ic.cam.position.z = -maxD * ic.camMaxDFactor; // forperspective, the z positionshould be large enough to see the whole molecule
                 }
 
-                if(ic.opts['slab'] === 'yes') {
-                    if(bInstance) {
-                        ic.cam.near = 0.1;
-                    }
-                    else if(ic.camMaxDFactorFog !== undefined) {
-                        ic.cam.near = maxD * ic.camMaxDFactorFog - 10; // keep some surrounding residues
-                    }
-                    else {
-                        ic.cam.near = maxD * ic.camMaxDFactor;
-                    }
-                }
-                else {
+                // if(ic.opts['slab'] === 'yes') {
+                //     if(bInstance) {
+                //         ic.cam.near = 0.1;
+                //     }
+                //     else if(ic.camMaxDFactorFog !== undefined) {
+                //         ic.cam.near = maxD * ic.camMaxDFactorFog - 10; // keep some surrounding residues
+                //     }
+                //     else {
+                //         ic.cam.near = maxD * ic.camMaxDFactor;
+                //     }
+                // }
+                // else {
                     ic.cam.near = 0.1;
-                }
+                // }
                 ic.cam.far = 10000;
 
                 if(ic.bControlGl && !me.bNode) {
@@ -76445,7 +76453,8 @@ class Camera {
                     }
                 }
             }
-            else if (ic.cam === ic.orthographicCamera){
+            // else if (ic.cam === ic.orthographicCamera){
+            else if(ic.opts.camera.toLowerCase() == 'orthographic') {
                 if(ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > 10 * ic.maxatomcnt) {
                     ic.cam.right = ic.maxD/2 * 1.5;
                 }
@@ -76457,12 +76466,12 @@ class Camera {
                 ic.cam.top = ic.cam.right /ic.container.whratio;
                 ic.cam.bottom = -ic.cam.right /ic.container.whratio;
 
-                  if(ic.opts['slab'] === 'yes') {
-                      ic.cam.near = ic.maxD * 2;
-                  }
-                  else {
+                //   if(ic.opts['slab'] === 'yes') {
+                //       ic.cam.near = ic.maxD * 2;
+                //   }
+                //   else {
                     ic.cam.near = 0;
-                  }
+                //   }
 
                   ic.cam.far = 10000;
 
@@ -76484,6 +76493,85 @@ class Camera {
             ic.cam.updateProjectionMatrix();
     //    }
     }
+
+    setSlab() { let ic = this.icn3d, me = ic.icn3dui;
+        if(ic.bControlGl && !me.bNode) {
+            let maxD = ic.maxD;
+
+            // if(window.cam === ic.perspectiveCamera) {
+            if(ic.opts.camera.toLowerCase() == 'perspective') {
+                let bInstance = (ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > ic.maxatomcnt) ? true : false;
+
+                if(ic.opts['slab'] === 'yes') {
+                    if(bInstance) {
+                        window.cam.near = 0.1;
+                    }
+                    else if(window.camMaxDFactorFog !== undefined) {
+                        window.cam.near = maxD * window.camMaxDFactorFog - 10; // keep some surrounding residues
+                    }
+                    else {
+                        window.cam.near = maxD * window.camMaxDFactor;
+                    }
+                }
+                else {
+                    window.cam.near = 0.1;
+                }
+            }
+            // else if (window.cam === ic.orthographicCamera){
+            else if(ic.opts.camera.toLowerCase() == 'orthographic') {
+                  if(ic.opts['slab'] === 'yes') {
+                      window.cam.near = ic.maxD * 2;
+                  }
+                  else {
+                    window.cam.near = 0;
+                  }
+
+                  window.cam.far = 10000;
+            }
+
+            window.cam.updateProjectionMatrix();
+        }
+    //    else {
+            // also set its own camera for picking purpose
+
+            let maxD = ic.maxD;
+
+            // if(ic.cam === ic.perspectiveCamera) {
+            if(ic.opts.camera.toLowerCase() == 'perspective') {
+                let bInstance = (ic.biomtMatrices !== undefined && ic.biomtMatrices.length * ic.cnt > ic.maxatomcnt) ? true : false;
+
+                if(ic.opts['slab'] === 'yes') {
+                    if(bInstance) {
+                        ic.cam.near = 0.1;
+                    }
+                    else if(ic.camMaxDFactorFog !== undefined) {
+                        ic.cam.near = maxD * ic.camMaxDFactorFog - 10; // keep some surrounding residues
+                    }
+                    else {
+                        ic.cam.near = maxD * ic.camMaxDFactor;
+                    }
+                }
+                else {
+                    ic.cam.near = 0.1;
+                }
+            }
+            // else if (ic.cam === ic.orthographicCamera){
+            else if(ic.opts.camera.toLowerCase() == 'orthographic') {
+                  if(ic.opts['slab'] === 'yes') {
+                      ic.cam.near = ic.maxD * 2;
+                  }
+                  else {
+                    ic.cam.near = 0;
+                  }
+
+                  ic.cam.far = 10000;
+            }
+
+            // ic.cam.add(ic.directionalLight);
+
+            ic.cam.updateProjectionMatrix();
+    //    }
+    }
 }
 
 /**
@@ -92620,7 +92708,7 @@ class AnnoSnpClinVar {
           let snpResn = snpStr.substr(posSymbol - 1, 1);
           let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[chnid + '_' + realResi]);
           let oneLetterRes = (atom) ? me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3)) : '';
-          if(!bFromClinVarDb) {
+          if(!bFromClinVarDb && ic.chainsSeq[chnid][resi - 1]) {
             oneLetterRes = ic.chainsSeq[chnid][resi - 1].name;
           }
 
@@ -118752,19 +118840,7 @@ class LoadScript {
     updateTransformation(steps) { let ic = this.icn3d; ic.icn3dui;
       let commandTransformation = (ic.commands[steps-1]) ? ic.commands[steps-1].split('|||') : [];
 
-      if(commandTransformation.length == 2) {
-          let transformation = JSON.parse(commandTransformation[1]);
-
-          ic._zoomFactor = transformation.factor;
-
-          ic.mouseChange.x = transformation.mouseChange.x;
-          ic.mouseChange.y = transformation.mouseChange.y;
-
-          ic.quaternion._x = transformation.quaternion._x;
-          ic.quaternion._y = transformation.quaternion._y;
-          ic.quaternion._z = transformation.quaternion._z;
-          ic.quaternion._w = transformation.quaternion._w;
-      }
+      ic.transformCls.resetOrientation_base(commandTransformation);
 
       // ic.bRender = true;
       ic.drawCls.draw();
@@ -119546,19 +119622,17 @@ class LoadScript {
 
         let commandTransformation = (ic.commands[steps-1]) ? ic.commands[steps-1].split('|||') : [];
 
-        if(commandTransformation.length == 2) {
-            let transformation = JSON.parse(commandTransformation[1]);
-
-            ic._zoomFactor = transformation.factor;
+        // load a URL with trackball transformation, or no info after "|||"
+        if(commandTransformation.length != 2 || (commandTransformation.length == 2 && commandTransformation[1].substr(0,1) == '{')) {
+          ic.bSetCamera = true;
+        } 
+        else {
+          ic.bSetCamera = false;
+        }
 
-            ic.mouseChange.x = transformation.mouseChange.x;
-            ic.mouseChange.y = transformation.mouseChange.y;
+        if(commandTransformation.length == 2 && commandTransformation[1].substr(0,1) == '{') ic.bTransformation = true;
 
-            ic.quaternion._x = transformation.quaternion._x;
-            ic.quaternion._y = transformation.quaternion._y;
-            ic.quaternion._z = transformation.quaternion._z;
-            ic.quaternion._w = transformation.quaternion._w;
-        }
+        ic.transformCls.resetOrientation_base(commandTransformation);
 
         ic.selectionCls.oneStructurePerWindow();
 
@@ -127960,13 +128034,9 @@ class Transform {
         this.icn3d = icn3d;
     }
 
-    //Set the orientation to the original one, but leave the style, color, etc alone.
-    resetOrientation() { let ic = this.icn3d; ic.icn3dui;
-        let bSet = false;
-        if(ic.commands.length > 0) {
-            let commandTransformation = ic.commands[0].split('|||');
-
-            if(commandTransformation.length == 2) {
+    resetOrientation_base(commandTransformation) { let ic = this.icn3d; ic.icn3dui;
+        if(commandTransformation.length == 2 && commandTransformation[1].length > 0) {
+            if(ic.bSetCamera) { // |||{"factor"...}
                 let transformation = JSON.parse(commandTransformation[1]);
 
                 ic._zoomFactor = transformation.factor;
@@ -127978,16 +128048,46 @@ 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('|');
+                bcfArray.forEach(item => {
+                    let itemArray = item.split(':');
+                    if(itemArray[0] == 'fov') {
+                        ic.cam.fov = parseFloat(itemArray[1]);
+                    }
+                    else {
+                        let abc = itemArray[1].split(',');
+                        if(itemArray[0] == 'pos') {
+                            ic.cam.position.set(parseFloat(abc[0]), parseFloat(abc[1]), parseFloat(abc[2]));
+                        }
+                        else if(itemArray[0] == 'dir') {
+                            ic.cam.quaternion.setFromUnitVectors(new Vector3$1(0, 0, -1), new Vector3$1(parseFloat(abc[0]), parseFloat(abc[1]), parseFloat(abc[2])));
+                        }
+                        else if(itemArray[0] == 'up') {
+                            ic.cam.up.set(parseFloat(abc[0]), parseFloat(abc[1]), parseFloat(abc[2]));
+                        }
+                    }
+                });
+
 
-                bSet = true;
             }
         }
-
-        if(!bSet) {
+        else {
             ic._zoomFactor = 1.0;
             ic.mouseChange = new Vector2$1(0,0);
             ic.quaternion = new Quaternion(0,0,0,1);
         }
+    }
+
+    //Set the orientation to the original one, but leave the style, color, etc alone.
+    resetOrientation() { let ic = this.icn3d; ic.icn3dui;
+        if(ic.commands.length > 0) {
+            let commandTransformation = ic.commands[0].split('|||');
+
+            this.resetOrientation_base(commandTransformation);
+        }
 
         //reset ic.maxD
         ic.maxD = ic.oriMaxD;
@@ -128217,25 +128317,43 @@ class Transform {
     }
 
     getTransformationStr(transformation) {var ic = this.icn3d; ic.icn3dui;
-        let transformation2 = {"factor": 1.0, "mouseChange": {"x": 0, "y": 0}, "quaternion": {"_x": 0, "_y": 0, "_z": 0, "_w": 1} };
-        transformation2.factor = parseFloat(transformation.factor).toPrecision(4);
-        transformation2.mouseChange.x = parseFloat(transformation.mouseChange.x).toPrecision(4);
-        transformation2.mouseChange.y = parseFloat(transformation.mouseChange.y).toPrecision(4);
-        transformation2.quaternion._x = parseFloat(transformation.quaternion._x).toPrecision(4);
-        transformation2.quaternion._y = parseFloat(transformation.quaternion._y).toPrecision(4);
-        transformation2.quaternion._z = parseFloat(transformation.quaternion._z).toPrecision(4);
-        transformation2.quaternion._w = parseFloat(transformation.quaternion._w).toPrecision(4);
-
-        if(transformation2.factor == '1.0000') transformation2.factor = 1;
-        if(transformation2.mouseChange.x == '0.0000') transformation2.mouseChange.x = 0;
-        if(transformation2.mouseChange.y == '0.0000') transformation2.mouseChange.y = 0;
-
-        if(transformation2.quaternion._x == '0.0000') transformation2.quaternion._x = 0;
-        if(transformation2.quaternion._y == '0.0000') transformation2.quaternion._y = 0;
-        if(transformation2.quaternion._z == '0.0000') transformation2.quaternion._z = 0;
-        if(transformation2.quaternion._w == '1.0000') transformation2.quaternion._w = 1;
-
-        return JSON.stringify(transformation2);
+        if(ic.bTransformation) {
+            let transformation2 = {"factor": 1.0, "mouseChange": {"x": 0, "y": 0}, "quaternion": {"_x": 0, "_y": 0, "_z": 0, "_w": 1} };
+            transformation2.factor = parseFloat(transformation.factor).toPrecision(4);
+            transformation2.mouseChange.x = parseFloat(transformation.mouseChange.x).toPrecision(4);
+            transformation2.mouseChange.y = parseFloat(transformation.mouseChange.y).toPrecision(4);
+            transformation2.quaternion._x = parseFloat(transformation.quaternion._x).toPrecision(4);
+            transformation2.quaternion._y = parseFloat(transformation.quaternion._y).toPrecision(4);
+            transformation2.quaternion._z = parseFloat(transformation.quaternion._z).toPrecision(4);
+            transformation2.quaternion._w = parseFloat(transformation.quaternion._w).toPrecision(4);
+
+            if(transformation2.factor == '1.0000') transformation2.factor = 1;
+            if(transformation2.mouseChange.x == '0.0000') transformation2.mouseChange.x = 0;
+            if(transformation2.mouseChange.y == '0.0000') transformation2.mouseChange.y = 0;
+
+            if(transformation2.quaternion._x == '0.0000') transformation2.quaternion._x = 0;
+            if(transformation2.quaternion._y == '0.0000') transformation2.quaternion._y = 0;
+            if(transformation2.quaternion._z == '0.0000') transformation2.quaternion._z = 0;
+            if(transformation2.quaternion._w == '1.0000') transformation2.quaternion._w = 1;
+
+            return JSON.stringify(transformation2);
+        }
+        else if(ic.cam) {
+            // |||pos:a,b,c|dir:a,b,c|up:a,b,c|fov:a
+            let str = '';
+            str += 'pos:' + ic.cam.position.x.toPrecision(4) + ',' + ic.cam.position.y.toPrecision(4) + ',' + ic.cam.position.z.toPrecision(4);
+
+            let direction = (new Vector3$1(0, 0, -1)).applyQuaternion(ic.cam.quaternion);
+            str += '|dir:' + direction.x.toPrecision(4) + ',' + direction.y.toPrecision(4) + ',' + direction.z.toPrecision(4);
+
+            str += '|up:' + ic.cam.up.x.toPrecision(4) + ',' + ic.cam.up.y.toPrecision(4) + ',' + ic.cam.up.z.toPrecision(4);
+            str += '|fov:' + ic.cam.fov.toPrecision(4);
+
+            return str;
+        }
+        else {
+            return '';
+        }
     }
 }
 
@@ -131150,38 +131268,14 @@ class Picking {
           else {
               // highlight the sequence background
               ic.hlUpdateCls.updateHlAll();
-              let transformation = {};
-              transformation.factor = ic._zoomFactor;
-              transformation.mouseChange = ic.mouseChange;
-              //transformation.quaternion = ic.quaternion;
-              transformation.quaternion = {};
-              transformation.quaternion._x = parseFloat(ic.quaternion._x).toPrecision(5);
-              transformation.quaternion._y = parseFloat(ic.quaternion._y).toPrecision(5);
-              transformation.quaternion._z = parseFloat(ic.quaternion._z).toPrecision(5);
-              transformation.quaternion._w = parseFloat(ic.quaternion._w).toPrecision(5);
-
-              /*
-              if(ic.bAddCommands) {
-                  ic.commands.push('pickatom ' + atom.serial + '|||' + ic.transformCls.getTransformationStr(transformation));
-                  ic.optsHistory.push(me.hashUtilsCls.cloneHash(ic.opts));
-                  ic.optsHistory[ic.optsHistory.length - 1].hlatomcount = Object.keys(ic.hAtoms).length;
-                  if(me.utilsCls.isSessionStorageSupported()) ic.setStyleCls.saveCommandsToSession();
-                  ic.STATENUMBER = ic.commands.length;
-              }
-              ic.logs.push('pickatom ' + atom.serial + '(chain: ' + atom.structure + '_' + atom.chain + ', residue: ' + atom.resn + ', number: ' + atom.resi + ', atom: ' + atom.name + ')');
-              if( $( "#" + ic.pre + "logtext" ).length )  {
-                $("#" + ic.pre + "logtext").val("> " + ic.logs.join("\n> ") + "\n> ").scrollTop($("#" + ic.pre + "logtext")[0].scrollHeight);
-              }
-              */
+
               me.htmlCls.clickMenuCls.setLogCmd('pickatom ' + atom.serial, true);
 
               ic.selectionCls.saveSelInCommand();
 
               // update the interaction flag
               ic.bSphereCalc = false;
-              //me.htmlCls.clickMenuCls.setLogCmd('set calculate sphere false', true);
               ic.bHbondCalc = false;
-              //me.htmlCls.clickMenuCls.setLogCmd('set calculate hbond false', true);
           }
       }
     }
@@ -131975,6 +132069,8 @@ class iCn3D {
 
     this.bUsePdbNum = true;
 
+    this.bSetCamera = true; 
+
     let bWebGL, bWebGL2, bVR;
     if(!this.icn3dui.bNode) {
         let canvas = document.createElement( 'canvas' );
@@ -132674,10 +132770,10 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.44.2';
+    this.REVISION = '3.45.0';
 
-    // In nodejs, iCn3D defines "window = {navigator: {}}"
-    this.bNode = (Object.keys(window).length < 2) ? true : false;
+    // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
+    this.bNode = (Object.keys(window).length < 3) ? true : false;
 
     if(this.cfg.command === undefined) this.cfg.command = '';
     if(this.cfg.width === undefined) this.cfg.width = '100%';