molstar 2.3.3 → 2.3.8

package/lib/extensions/rcsb/validation-report/representation.js

@@ -38,7 +38,7 @@ function createIntraUnitClashCylinderMesh(ctx, unit, structure, theme, props, me
             pos(elements[a[edgeIndex]], posA);
             pos(elements[b[edgeIndex]], posB);
         },
-        style: function (edgeIndex) { return 4 /* Disk */; },
+        style: function (edgeIndex) { return 6 /* Disk */; },
         radius: function (edgeIndex) { return magnitude[edgeIndex] * sizeFactor; },
     };
     return createLinkCylinderMesh(ctx, builderProps, props, mesh);
@@ -74,7 +74,7 @@ function getIntraClashLabel(structure, unit, clashes, elements) {
     var mag = magnitude[idx].toFixed(2);
     var dist = distance[idx].toFixed(2);
     return [
-        "Clash id: " + id[idx] + " | Magnitude: " + mag + " \u212B | Distance: " + dist + " \u212B",
+        "Clash id: ".concat(id[idx], " | Magnitude: ").concat(mag, " \u212B | Distance: ").concat(dist, " \u212B"),
         bondLabel(Bond.Location(structure, unit, clashes.a[idx], structure, unit, clashes.b[idx]))
     ].join('</br>');
 }
@@ -130,7 +130,7 @@ function createInterUnitClashCylinderMesh(ctx, structure, theme, props, mesh) {
             uA.conformation.position(uA.elements[b.indexA], posA);
             uB.conformation.position(uB.elements[b.indexB], posB);
         },
-        style: function (edgeIndex) { return 4 /* Disk */; },
+        style: function (edgeIndex) { return 6 /* Disk */; },
         radius: function (edgeIndex) { return edges[edgeIndex].props.magnitude * sizeFactor; }
     };
     return createLinkCylinderMesh(ctx, builderProps, props, mesh);
@@ -171,7 +171,7 @@ function getInterClashLabel(structure, clashes, elements) {
     var mag = c.props.magnitude.toFixed(2);
     var dist = c.props.distance.toFixed(2);
     return [
-        "Clash id: " + c.props.id + " | Magnitude: " + mag + " \u212B | Distance: " + dist + " \u212B",
+        "Clash id: ".concat(c.props.id, " | Magnitude: ").concat(mag, " \u212B | Distance: ").concat(dist, " \u212B"),
         bondLabel(Bond.Location(structure, uA, c.indexA, structure, uB, c.indexB))
     ].join('</br>');
 }

package/lib/extensions/rcsb/validation-report/representation.js.map

@@ -1 +1 @@
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package/lib/mol-canvas3d/camera/util.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -25,6 +25,7 @@ declare namespace Viewport {
 export declare function cameraProject(out: Vec4, point: Vec3, viewport: Viewport, projectionView: Mat4): Vec4;
 /**
  * Transform point from screen space to 3D coordinates.
- * The point must have x and y set to 2D window coordinates and z between 0 (near) and 1 (far).
+ * The point must have `x` and `y` set to 2D window coordinates
+ * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
  */
-export declare function cameraUnproject(out: Vec3, point: Vec3, viewport: Viewport, inverseProjectionView: Mat4): Vec3;
+export declare function cameraUnproject(out: Vec3, point: Vec3 | Vec4, viewport: Viewport, inverseProjectionView: Mat4): Vec3;

package/lib/mol-canvas3d/camera/util.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -48,12 +48,10 @@ function Viewport() {
     Viewport.equals = equals;
 })(Viewport || (Viewport = {}));
 //
-var NEAR_RANGE = 0;
-var FAR_RANGE = 1;
 var tmpVec4 = Vec4();
 /** Transform point into 2D window coordinates. */
 export function cameraProject(out, point, viewport, projectionView) {
-    var vX = viewport.x, vY = viewport.y, vWidth = viewport.width, vHeight = viewport.height;
+    var x = viewport.x, y = viewport.y, width = viewport.width, height = viewport.height;
     // clip space -> NDC -> window coordinates, implicit 1.0 for w component
     Vec4.set(tmpVec4, point[0], point[1], point[2], 1.0);
     // transform into clip space
@@ -65,25 +63,26 @@ export function cameraProject(out, point, viewport, projectionView) {
         tmpVec4[1] /= w;
         tmpVec4[2] /= w;
     }
-    // transform into window coordinates, set fourth component is (1/clip.w) as in gl_FragCoord.w
-    out[0] = vX + vWidth / 2 * tmpVec4[0] + (0 + vWidth / 2);
-    out[1] = vY + vHeight / 2 * tmpVec4[1] + (0 + vHeight / 2);
-    out[2] = (FAR_RANGE - NEAR_RANGE) / 2 * tmpVec4[2] + (FAR_RANGE + NEAR_RANGE) / 2;
+    // transform into window coordinates, set fourth component to 1 / clip.w as in gl_FragCoord.w
+    out[0] = (tmpVec4[0] + 1) * width * 0.5 + x;
+    out[1] = (1 - tmpVec4[1]) * height * 0.5 + y; // flip Y
+    out[2] = (tmpVec4[2] + 1) * 0.5;
     out[3] = w === 0 ? 0 : 1 / w;
     return out;
 }
 /**
  * Transform point from screen space to 3D coordinates.
- * The point must have x and y set to 2D window coordinates and z between 0 (near) and 1 (far).
+ * The point must have `x` and `y` set to 2D window coordinates
+ * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
  */
 export function cameraUnproject(out, point, viewport, inverseProjectionView) {
-    var vX = viewport.x, vY = viewport.y, vWidth = viewport.width, vHeight = viewport.height;
-    var x = point[0] - vX;
-    var y = (vHeight - point[1] - 1) - vY;
-    var z = point[2];
-    out[0] = (2 * x) / vWidth - 1;
-    out[1] = (2 * y) / vHeight - 1;
-    out[2] = 2 * z - 1;
+    var x = viewport.x, y = viewport.y, width = viewport.width, height = viewport.height;
+    var px = point[0] - x;
+    var py = (height - point[1] - 1) - y;
+    var pz = point[2];
+    out[0] = (2 * px) / width - 1;
+    out[1] = (2 * py) / height - 1;
+    out[2] = 2 * pz - 1;
     return Vec3.transformMat4(out, out, inverseProjectionView);
 }
 //# sourceMappingURL=util.js.map

package/lib/mol-canvas3d/camera/util.js.map

@@ -1 +1 @@
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package/lib/mol-canvas3d/camera.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -57,8 +57,16 @@ declare class Camera implements ICamera {
     getFocus(target: Vec3, radius: number, up?: Vec3, dir?: Vec3): Partial<Camera.Snapshot>;
     getInvariantFocus(target: Vec3, radius: number, up: Vec3, dir: Vec3): Partial<Camera.Snapshot>;
     focus(target: Vec3, radius: number, durationMs?: number, up?: Vec3, dir?: Vec3): void;
+    /** Transform point into 2D window coordinates. */
     project(out: Vec4, point: Vec3): Vec4;
-    unproject(out: Vec3, point: Vec3): Vec3;
+    /**
+     * Transform point from screen space to 3D coordinates.
+     * The point must have `x` and `y` set to 2D window coordinates
+     * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
+     */
+    unproject(out: Vec3, point: Vec3 | Vec4): Vec3;
+    /** World space pixel size at given `point` */
+    getPixelSize(point: Vec3): number;
     constructor(state?: Partial<Camera.Snapshot>, viewport?: Viewport, props?: Partial<{
         pixelScale: number;
     }>);
@@ -69,7 +77,7 @@ declare namespace Camera {
     /**
      * Sets an offseted view in a larger frustum. This is useful for
      * - multi-window or multi-monitor/multi-machine setups
-     * - jittering the camera position for
+     * - jittering the camera position for sampling
      */
     interface ViewOffset {
         enabled: boolean;

package/lib/mol-canvas3d/camera.js

@@ -1,14 +1,17 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-import { Mat4, Vec3, EPSILON } from '../mol-math/linear-algebra';
+import { Mat4, Vec3, Vec4, EPSILON } from '../mol-math/linear-algebra';
 import { Viewport, cameraProject, cameraUnproject } from './camera/util';
 import { CameraTransitionManager } from './camera/transition';
 import { BehaviorSubject } from 'rxjs';
 export { Camera };
+var tmpPos1 = Vec3();
+var tmpPos2 = Vec3();
+var tmpClip = Vec4();
 var Camera = /** @class */ (function () {
     function Camera(state, viewport, props) {
         if (viewport === void 0) { viewport = Viewport.create(0, 0, 128, 128); }
@@ -135,12 +138,29 @@ var Camera = /** @class */ (function () {
             this.setState(this.getFocus(target, radius, up, dir), durationMs);
         }
     };
+    /** Transform point into 2D window coordinates. */
     Camera.prototype.project = function (out, point) {
         return cameraProject(out, point, this.viewport, this.projectionView);
     };
+    /**
+     * Transform point from screen space to 3D coordinates.
+     * The point must have `x` and `y` set to 2D window coordinates
+     * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
+     */
     Camera.prototype.unproject = function (out, point) {
         return cameraUnproject(out, point, this.viewport, this.inverseProjectionView);
     };
+    /** World space pixel size at given `point` */
+    Camera.prototype.getPixelSize = function (point) {
+        // project -> unproject of `point` does not exactly return the same
+        // to get a sufficiently accurate measure we unproject the original
+        // clip position in addition to the one shifted bey one pixel
+        this.project(tmpClip, point);
+        this.unproject(tmpPos1, tmpClip);
+        tmpClip[0] += 1;
+        this.unproject(tmpPos2, tmpClip);
+        return Vec3.distance(tmpPos1, tmpPos2);
+    };
     return Camera;
 }());
 (function (Camera) {

package/lib/mol-canvas3d/camera.js.map

@@ -1 +1 @@
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package/lib/mol-canvas3d/canvas3d.d.ts

@@ -141,6 +141,10 @@ export declare const Canvas3DParams: {
             maxDistanceMin: any;
         }>, "on">;
     }>>;
+    interaction: PD.Group<PD.Normalize<{
+        maxFps: number;
+        preferAtomPixelPadding: number;
+    }>>;
     debug: PD.Group<PD.Normalize<{
         sceneBoundingSpheres: boolean;
         visibleSceneBoundingSpheres: boolean;
@@ -283,6 +287,10 @@ export declare const DefaultCanvas3DParams: PD.Values<{
             maxDistanceMin: any;
         }>, "on">;
     }>>;
+    interaction: PD.Group<PD.Normalize<{
+        maxFps: number;
+        preferAtomPixelPadding: number;
+    }>>;
     debug: PD.Group<PD.Normalize<{
         sceneBoundingSpheres: boolean;
         visibleSceneBoundingSpheres: boolean;
@@ -334,6 +342,8 @@ declare namespace Canvas3DContext {
         preserveDrawingBuffer: boolean;
         pixelScale: number;
         pickScale: number;
+        /** extra pixels to around target to check in case target is empty */
+        pickPadding: number;
         enableWboit: boolean;
         preferWebGl1: boolean;
     };

package/lib/mol-canvas3d/canvas3d.js

@@ -20,7 +20,7 @@ import { Camera } from './camera';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { DebugHelperParams } from './helper/bounding-sphere-helper';
 import { SetUtils } from '../mol-util/set';
-import { Canvas3dInteractionHelper } from './helper/interaction-events';
+import { Canvas3dInteractionHelper, Canvas3dInteractionHelperParams } from './helper/interaction-events';
 import { PostprocessingParams } from './passes/postprocessing';
 import { MultiSampleHelper, MultiSampleParams, MultiSamplePass } from './passes/multi-sample';
 import { PickHelper } from './passes/pick';
@@ -77,6 +77,7 @@ export var Canvas3DParams = {
     marking: PD.Group(MarkingParams),
     renderer: PD.Group(RendererParams),
     trackball: PD.Group(TrackballControlsParams),
+    interaction: PD.Group(Canvas3dInteractionHelperParams),
     debug: PD.Group(DebugHelperParams),
     handle: PD.Group(HandleHelperParams),
 };
@@ -91,6 +92,8 @@ var Canvas3DContext;
         preserveDrawingBuffer: true,
         pixelScale: 1,
         pickScale: 0.25,
+        /** extra pixels to around target to check in case target is empty */
+        pickPadding: 1,
         enableWboit: true,
         preferWebGl1: false
     };
@@ -208,8 +211,8 @@ var Canvas3D;
         var controls = TrackballControls.create(input, camera, p.trackball);
         var renderer = Renderer.create(webgl, p.renderer);
         var helper = new Helper(webgl, scene, p);
-        var pickHelper = new PickHelper(webgl, renderer, scene, helper, passes.pick, { x: x, y: y, width: width, height: height });
-        var interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input, camera);
+        var pickHelper = new PickHelper(webgl, renderer, scene, helper, passes.pick, { x: x, y: y, width: width, height: height }, attribs.pickPadding);
+        var interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input, camera, p.interaction);
         var multiSampleHelper = new MultiSampleHelper(passes.multiSample);
         var cameraResetRequested = false;
         var nextCameraResetDuration = void 0;
@@ -438,9 +441,9 @@ var Canvas3D;
             console.log(webgl.stats);
             var _a = webgl.resources.getByteCounts(), texture = _a.texture, attribute = _a.attribute, elements = _a.elements;
             console.log({
-                texture: (texture / 1024 / 1024).toFixed(3) + " MiB",
-                attribute: (attribute / 1024 / 1024).toFixed(3) + " MiB",
-                elements: (elements / 1024 / 1024).toFixed(3) + " MiB",
+                texture: "".concat((texture / 1024 / 1024).toFixed(3), " MiB"),
+                attribute: "".concat((attribute / 1024 / 1024).toFixed(3), " MiB"),
+                elements: "".concat((elements / 1024 / 1024).toFixed(3), " MiB"),
             });
         }
         function add(repr) {
@@ -514,6 +517,7 @@ var Canvas3D;
                 multiSample: __assign({}, p.multiSample),
                 renderer: __assign({}, renderer.props),
                 trackball: __assign({}, controls.props),
+                interaction: __assign({}, interactionHelper.props),
                 debug: __assign({}, helper.debug.props),
                 handle: __assign({}, helper.handle.props),
             };
@@ -657,6 +661,8 @@ var Canvas3D;
                     renderer.setProps(props.renderer);
                 if (props.trackball)
                     controls.setProps(props.trackball);
+                if (props.interaction)
+                    interactionHelper.setProps(props.interaction);
                 if (props.debug)
                     helper.debug.setProps(props.debug);
                 if (props.handle)

package/lib/mol-canvas3d/canvas3d.js.map

@@ -1 +1 @@
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package/lib/mol-canvas3d/helper/handle-helper.js

@@ -154,7 +154,7 @@ export var HandleGroup = {
     // RotateObjectZ: 12,
 };
 function HandleLoci(handleHelper, groupId, instanceId) {
-    return DataLoci('handle', handleHelper, [{ groupId: groupId, instanceId: instanceId }], function (boundingSphere) { return handleHelper.getBoundingSphere(boundingSphere, instanceId); }, function () { return "Handle Helper | Group Id " + groupId + " | Instance Id " + instanceId; });
+    return DataLoci('handle', handleHelper, [{ groupId: groupId, instanceId: instanceId }], function (boundingSphere) { return handleHelper.getBoundingSphere(boundingSphere, instanceId); }, function () { return "Handle Helper | Group Id ".concat(groupId, " | Instance Id ").concat(instanceId); });
 }
 export function isHandleLoci(x) {
     return x.kind === 'data-loci' && x.tag === 'handle';