icn3d 3.54.1 → 3.54.3

package/icn3d.module.js

@@ -57640,7 +57640,7 @@ class SubdivideCls {
 
     // cubic splines for four points: http://thalestriangles.blogspot.com/2014/02/a-bit-of-ex-spline-ation.html
     // https://math.stackexchange.com/questions/577641/how-to-calculate-interpolating-splines-in-3d-space
-    subdivide(_pnts, _clrs, DIV) { let me = this.icn3dui;
+    subdivide(_pnts, _clrs, DIV, bOld) { let me = this.icn3dui;
 
         let ret = [];
         let pos = [];
@@ -57723,6 +57723,16 @@ class SubdivideCls {
         savedColor = [];
         pnts = [];
 
+        // adjust the color
+        if(!bOld) {
+            let half = Math.floor(DIV / 2);
+            for(let i = 0, il = color.length; i < il; ++i) {
+                let j = i + half;
+                if(j > il - 1) j = il - 1;
+                color[i] = color[j];
+            }
+        }
+  
         pnts_positions.push(ret);
         pnts_positions.push(pos);
         pnts_positions.push(color);
@@ -79134,6 +79144,7 @@ class CurveStripArrow {
         // use the sheet coord for n-2 residues
         let colorsTmp = [];
         let extraArrow = (bStrip) ? 2 : 0; // extend the tube by 5 sub-points into a preceding/following helix/sheet
+//        let extraArrow = (bStrip) ? 0 : 0; // extend the tube by 5 sub-points into a preceding/following helix/sheet
 
         let i, lastIndex = (bShowArrow === undefined || bShowArrow) ? pntsCA.length - ic.axisDIV + extraArrow : pntsCA.length;
 
@@ -79149,20 +79160,22 @@ class CurveStripArrow {
             posIndex.push(positions[i]); 
         }
 
-        if(bStrip) {
-            if(bHelix) {
-                ic.stripCls.createStrip(pnts[0], pnts[1], colorsTmp, div, thickness, bHighlight, true,
-                      undefined, posIndex, pntsCATmp, prevCOArrayTmp);
+//        if(!(bShowArrow === undefined || bShowArrow)) {
+            if(bStrip) {
+                if(bHelix) {
+                    ic.stripCls.createStrip(pnts[0], pnts[1], colorsTmp, div, thickness, bHighlight, true,
+                        undefined, posIndex, pntsCATmp, prevCOArrayTmp);
+                }
+                else {
+                    ic.stripCls.createStrip(pnts[0], pnts[1], colorsTmp, div, thickness, bHighlight, true,
+                    undefined, posIndex);
+                }
             }
             else {
-                ic.stripCls.createStrip(pnts[0], pnts[1], colorsTmp, div, thickness, bHighlight, true,
-                  undefined, posIndex);
+                ic.curveCls.createCurveSub(pnts[0], width, colorsTmp, div, bHighlight, bRibbon, true,
+                undefined, posIndex);
             }
-        }
-        else {
-            ic.curveCls.createCurveSub(pnts[0], width, colorsTmp, div, bHighlight, bRibbon, true,
-              undefined, posIndex);
-        }
+//        }
 
         if(bShowArrow === undefined || bShowArrow) {
             // draw the arrow
@@ -81141,7 +81154,8 @@ class Tube {
         let pnts;
 
         if(bSubdivide) {
-            let pnts_clrs = me.subdivideCls.subdivide(_pnts, colors, axisDiv);
+            let bOld = true;
+            let pnts_clrs = me.subdivideCls.subdivide(_pnts, colors, axisDiv, bOld);
 
             pnts = pnts_clrs[0];
             colors = pnts_clrs[2];
@@ -81388,7 +81402,7 @@ class Strand {
         let pntsCAAllSub = [], prevCOArrayAllSub = [], positionsSub = [], colorsAllSub = [];
 
         let currentChain, currentStyle, currentCA = null, currentColor = null, prevCoorCA = null, prevCoorO = null, prevColor = null;
-        let prevCO = null, ss = null, ssend = false, ssJoint = false, prevResi = null, prevResid = null;
+        let prevCO = null, ss = null, ssend = false, prevResi = null, prevResid = null;
         let strandWidth, bSheetSegment = false, bHelixSegment = false;
         let atom, tubeAtoms = [];
 
@@ -81490,10 +81504,15 @@ class Strand {
                         let delta = -1 + numM1Inv2 * j;
                         let v = new Vector3$1(prevCoorCA.x + prevCO.x * delta, prevCoorCA.y + prevCO.y * delta, prevCoorCA.z + prevCO.z * delta);
                         // no smoothen for the last two residues in sheet
-                        if (!doNotSmoothen && ss === 'sheet' && !ssJoint && !(atom.ssend)) v.smoothen = true;
+                        // if (!doNotSmoothen && ss === 'sheet' && !ssJoint && !(atom.ssend)) v.smoothen = true;
+                        if (!doNotSmoothen && ss === 'sheet') v.smoothen = true;
                         pntsAll[j].push(v);
                     }
 
+                    if (!doNotSmoothen && ss === 'sheet') {
+                        prevCoorCA.smoothen = true;
+                        prevCO.smoothen = true;
+                    }
                     pntsCAAll.push(prevCoorCA);
                     prevCOArrayAll.push(prevCO);
                 }
@@ -81507,7 +81526,7 @@ class Strand {
 
                 ss = atom.ss;
                 ssend = atom.ssend;
-                ssJoint = atom.ssbegin || atom.ssend;
+                atom.ssbegin || atom.ssend;
             } // end if (atom.name === 'O' || (ic.bCalphaOnly && atom.name === 'CA') ) {
           } // end if ((atom.name === 'O' || atom.name === 'CA') && !atom.het) {
         } // end for
@@ -81521,9 +81540,14 @@ class Strand {
             let delta = -1 + numM1Inv2 * j;
             let v = new Vector3$1(prevCoorCA.x + prevCO.x * delta, prevCoorCA.y + prevCO.y * delta, prevCoorCA.z + prevCO.z * delta);
             // no smoothen for the last two residues in sheet
-            if (!doNotSmoothen && ss === 'sheet' && !ssJoint && !(ssend)) v.smoothen = true;
+            //if (!doNotSmoothen && ss === 'sheet' && !ssJoint && !(ssend)) v.smoothen = true;
+            if (!doNotSmoothen && ss === 'sheet') v.smoothen = true;
             pntsAll[j].push(v);
         }
+        if (!doNotSmoothen && ss === 'sheet') {
+            prevCoorCA.smoothen = true;
+            prevCO.smoothen = true;
+        }
         pntsCAAll.push(prevCoorCA);
         prevCOArrayAll.push(prevCO);
 
@@ -81547,7 +81571,6 @@ class Strand {
         prevCoorCA = null;
         ss = null;
         ssend = false;
-        ssJoint = false;
 
         index = 0;
         let bLastResDrawn = false;
@@ -105703,9 +105726,37 @@ class WebGLPathTracer {
         ic.impostorCls.clearImpostors();
         
         if(ic.bRender && (!ic.hAtoms || Object.keys(ic.hAtoms) == 0)) ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
-
+/*
+        // save the current view when the URL used |||pos:...
+        let cam = (ic.bControlGl && !me.bNode) ? window.cam : ic.cam;
+        let controls = (ic.bControlGl && !me.bNode) ? window.controls : ic.controls;
+        let bKeepCamera = (!ic.bSetCamera || ic.bKeepCamera) && cam && controls && !me.bNode;
+
+        let camState;
+        if(bKeepCamera) {
+            camState = {
+                pos: cam.position.clone(), up: cam.up.clone(), quat: cam.quaternion.clone(),
+                target: controls.target.clone(), fov: cam.fov, zoom: cam.zoom,
+                left: cam.left, right: cam.right, top: cam.top, bottom: cam.bottom
+            };
+        }
+*/
         ic.sceneCls.rebuildScene();
-
+/*
+        // restore the saved  cam state
+        if(bKeepCamera) {
+            // setCamera() created new controls, so re-read them
+            //controls = (ic.bControlGl && !me.bNode) ? window.controls : ic.controls;
+            cam.position.copy(camState.pos);
+            cam.up.copy(camState.up);
+            cam.quaternion.copy(camState.quat);
+            controls.target.copy(camState.target);
+            cam.zoom = camState.zoom;
+            if(cam.isPerspectiveCamera) cam.fov = camState.fov;
+            cam.updateProjectionMatrix();
+            cam.updateMatrixWorld(true);
+        }
+*/
         // Impostor display using the saved arrays
         if(ic.bImpo) {
             ic.impostorCls.drawImpostorShader(); // target
@@ -105739,7 +105790,13 @@ class WebGLPathTracer {
               if($("#" + ic.pre + "cmdlog")) $("#" + ic.pre + "cmdlog").show();
           }
 
-          this.applyTransformation(ic._zoomFactor, ic.mouseChange, ic.quaternion);
+          if(ic.bSetCamera) {
+            this.applyTransformation(ic._zoomFactor, ic.mouseChange, ic.quaternion);
+          }
+          else {
+            let commandTransformation = ic.commands[ic.commands.length-1].split('|||');
+            ic.transformCls.resetOrientation_base(commandTransformation);
+          }
 
           this.render(bVrAr, bPathTracer);
         }
@@ -105892,14 +105949,7 @@ class WebGLPathTracer {
         ic.setOptionCls.setStyle("proteins", atom.style);
     }
 
-    //Render the scene and objects into pixels.
-    render_base(bPathTracer) { let ic = this.icn3d, me = ic.icn3dui;
-        let thisClass = this;
-
-        if(me.bNode) return;
-
-        let cam = (ic.bControlGl && !me.bNode) ? window.cam : ic.cam;
-
+    setDirectLight(cam) { let ic = this.icn3d; ic.icn3dui;
         if(ic.directionalLight) {
             let quaternion = new Quaternion();
             quaternion.setFromUnitVectors( new Vector3$1(0, 0, ic.cam_z).normalize(), cam.position.clone().normalize() );
@@ -105914,6 +105964,19 @@ class WebGLPathTracer {
             ic.directionalLight3.applyMatrix4(cam.matrixWorld);
         }
 
+        return cam;
+    }
+
+    //Render the scene and objects into pixels.
+    render_base(bPathTracer) { let ic = this.icn3d, me = ic.icn3dui;
+        let thisClass = this;
+
+        if(me.bNode) return;
+
+        let cam = (ic.bControlGl && !me.bNode) ? window.cam : ic.cam;
+
+        cam = this.setDirectLight(cam);
+
         if(!ic.bVr) ic.renderer.setPixelRatio( window.devicePixelRatio ); // r71
 
         if(ic.bVr) {
@@ -105955,8 +106018,14 @@ class WebGLPathTracer {
             else {
                 if(bPathTracer) {
                     ic.bImpo = false; // disable impostor for path tracing
+                    // remove the highlights since they are not 3D objects
+                    ic.hlUpdateCls.clearHighlight();
+
                     const pathTracer = new WebGLPathTracer(ic.renderer);
                     pathTracer.setScene(ic.scene, cam);
+
+                    cam = this.setDirectLight(cam);
+
                     //pathTracer.renderUpdates(); // Updates samples if the scene/camera changes
                     //pathTracer.render(ic.scene, cam);
 
@@ -154564,7 +154633,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.54.0';
+    this.REVISION = '3.54.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
     this.bNode = (Object.keys(window).length < 3) ? true : false;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "3.54.1",
+  "version": "3.54.3",
   "main": "./icn3d.js",
   "exports": {
     ".": {