molstar 2.3.8 → 3.0.0-dev.0

package/lib/mol-plugin-ui/viewport/simple-settings.js.map

@@ -1 +1 @@
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package/lib/mol-repr/representation.d.ts

@@ -20,6 +20,7 @@ import { Mat4 } from '../mol-math/linear-algebra';
 import { BaseGeometry } from '../mol-geo/geometry/base';
 import { CustomProperty } from '../mol-model-props/common/custom-property';
 import { Clipping } from '../mol-theme/clipping';
+import { Substance } from '../mol-theme/substance';
 export declare type RepresentationProps = {
     [k: string]: any;
 };
@@ -90,6 +91,7 @@ interface Representation<D, P extends PD.Params = {}, S extends Representation.S
     /** Number of addressable groups in all visuals of the representation */
     readonly groupCount: number;
     readonly renderObjects: ReadonlyArray<GraphicsRenderObject>;
+    readonly geometryVersion: number;
     readonly props: Readonly<PD.Values<P>>;
     readonly params: Readonly<P>;
     readonly state: Readonly<S>;
@@ -125,6 +127,8 @@ declare namespace Representation {
         overpaint: Overpaint;
         /** Per group transparency applied to the representation's renderobjects */
         transparency: Transparency;
+        /** Per group material applied to the representation's renderobjects */
+        substance: Substance;
         /** Bit mask of per group clipping applied to the representation's renderobjects */
         clipping: Clipping;
         /** Controls if the representation's renderobjects are synced automatically with GPU or not */
@@ -146,6 +150,14 @@ declare namespace Representation {
     type Def<D, P extends PD.Params = {}, S extends State = State> = {
         [k: string]: RepresentationFactory<D, P, S>;
     };
+    class GeometryState {
+        private curr;
+        private next;
+        private _version;
+        get version(): number;
+        add(id: number, version: number): void;
+        snapshot(): void;
+    }
     function createMulti<D, P extends PD.Params = {}, S extends State = State>(label: string, ctx: RepresentationContext, getParams: RepresentationParamsGetter<D, P>, stateBuilder: StateBuilder<S>, reprDefs: Def<D, P>): Representation<D, P, S>;
     function fromRenderObject(label: string, renderObject: GraphicsRenderObject): Representation<GraphicsRenderObject, BaseGeometry.Params>;
 }

package/lib/mol-repr/representation.js

@@ -19,6 +19,9 @@ import { getQualityProps } from './util';
 import { BaseGeometry } from '../mol-geo/geometry/base';
 import { Visual } from './visual';
 import { Clipping } from '../mol-theme/clipping';
+import { SetUtils } from '../mol-util/set';
+import { cantorPairing } from '../mol-data/util';
+import { Substance } from '../mol-theme/substance';
 export var RepresentationProvider;
 (function (RepresentationProvider) {
     function getDetaultParams(r, ctx, data) {
@@ -115,7 +118,7 @@ var Representation;
         Loci.Empty = { loci: EmptyLoci };
     })(Loci = Representation.Loci || (Representation.Loci = {}));
     function createState() {
-        return { visible: true, alphaFactor: 1, pickable: true, colorOnly: false, syncManually: false, transform: Mat4.identity(), overpaint: Overpaint.Empty, transparency: Transparency.Empty, clipping: Clipping.Empty, markerActions: MarkerActions.All };
+        return { visible: true, alphaFactor: 1, pickable: true, colorOnly: false, syncManually: false, transform: Mat4.identity(), overpaint: Overpaint.Empty, transparency: Transparency.Empty, substance: Substance.Empty, clipping: Clipping.Empty, markerActions: MarkerActions.All };
     }
     Representation.createState = createState;
     function updateState(state, update) {
@@ -131,6 +134,8 @@ var Representation;
             state.overpaint = update.overpaint;
         if (update.transparency !== undefined)
             state.transparency = update.transparency;
+        if (update.substance !== undefined)
+            state.substance = update.substance;
         if (update.clipping !== undefined)
             state.clipping = update.clipping;
         if (update.syncManually !== undefined)
@@ -143,7 +148,7 @@ var Representation;
     Representation.updateState = updateState;
     Representation.StateBuilder = { create: createState, update: updateState };
     Representation.Empty = {
-        label: '', groupCount: 0, renderObjects: [], props: {}, params: {}, updated: new Subject(), state: createState(), theme: Theme.createEmpty(),
+        label: '', groupCount: 0, renderObjects: [], geometryVersion: -1, props: {}, params: {}, updated: new Subject(), state: createState(), theme: Theme.createEmpty(),
         createOrUpdate: function () { return Task.constant('', undefined); },
         setState: function () { },
         setTheme: function () { },
@@ -151,10 +156,38 @@ var Representation;
         mark: function () { return false; },
         destroy: function () { }
     };
+    var GeometryState = /** @class */ (function () {
+        function GeometryState() {
+            this.curr = new Set();
+            this.next = new Set();
+            this._version = -1;
+        }
+        Object.defineProperty(GeometryState.prototype, "version", {
+            get: function () {
+                return this._version;
+            },
+            enumerable: false,
+            configurable: true
+        });
+        GeometryState.prototype.add = function (id, version) {
+            this.next.add(cantorPairing(id, version));
+        };
+        GeometryState.prototype.snapshot = function () {
+            var _a;
+            if (!SetUtils.areEqual(this.curr, this.next)) {
+                this._version += 1;
+            }
+            _a = [this.next, this.curr], this.curr = _a[0], this.next = _a[1];
+            this.next.clear();
+        };
+        return GeometryState;
+    }());
+    Representation.GeometryState = GeometryState;
     function createMulti(label, ctx, getParams, stateBuilder, reprDefs) {
         var _this = this;
         var version = 0;
         var updated = new Subject();
+        var geometryState = new GeometryState();
         var currentState = stateBuilder.create();
         var currentTheme = Theme.createEmpty();
         var currentParams;
@@ -194,6 +227,7 @@ var Representation;
                 }
                 return renderObjects;
             },
+            get geometryVersion() { return geometryState.version; },
             get props() { return currentProps; },
             get params() { return currentParams; },
             createOrUpdate: function (props, data) {
@@ -215,16 +249,20 @@ var Representation;
                                 i = 0, il = reprList.length;
                                 _a.label = 1;
                             case 1:
-                                if (!(i < il)) return [3 /*break*/, 4];
+                                if (!(i < il)) return [3 /*break*/, 5];
                                 if (!(!visuals || visuals.includes(reprMap[i]))) return [3 /*break*/, 3];
                                 return [4 /*yield*/, reprList[i].createOrUpdate(currentProps, currentData).runInContext(runtime)];
                             case 2:
                                 _a.sent();
                                 _a.label = 3;
                             case 3:
+                                geometryState.add(i, reprList[i].geometryVersion);
+                                _a.label = 4;
+                            case 4:
                                 ++i;
                                 return [3 /*break*/, 1];
-                            case 4:
+                            case 5:
+                                geometryState.snapshot();
                                 updated.next(version++);
                                 return [2 /*return*/];
                         }
@@ -254,7 +292,7 @@ var Representation;
             setState: function (state) {
                 stateBuilder.update(currentState, state);
                 for (var i = 0, il = reprList.length; i < il; ++i) {
-                    reprList[i].setState(currentState);
+                    reprList[i].setState(state); // only set the new (partial) state
                 }
             },
             setTheme: function (theme) {
@@ -275,6 +313,7 @@ var Representation;
         var _this = this;
         var version = 0;
         var updated = new Subject();
+        var geometryState = new GeometryState();
         var currentState = Representation.createState();
         var currentTheme = Theme.createEmpty();
         var currentParams = PD.clone(BaseGeometry.Params);
@@ -284,6 +323,7 @@ var Representation;
             updated: updated,
             get groupCount() { return renderObject.values.uGroupCount.ref.value; },
             get renderObjects() { return [renderObject]; },
+            get geometryVersion() { return geometryState.version; },
             get props() { return currentProps; },
             get params() { return currentParams; },
             createOrUpdate: function (props) {
@@ -293,6 +333,8 @@ var Representation;
                 return Task.create("Updating '".concat(label, "' representation"), function (runtime) { return __awaiter(_this, void 0, void 0, function () {
                     return __generator(this, function (_a) {
                         // TODO
+                        geometryState.add(0, renderObject.id);
+                        geometryState.snapshot();
                         updated.next(version++);
                         return [2 /*return*/];
                     });
@@ -323,6 +365,9 @@ var Representation;
                 if (state.transparency !== undefined) {
                     // TODO
                 }
+                if (state.substance !== undefined) {
+                    // TODO
+                }
                 if (state.transform !== undefined)
                     Visual.setTransform(renderObject, state.transform);
                 Representation.updateState(currentState, state);

package/lib/mol-repr/representation.js.map

@@ -1 +1 @@
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package/lib/mol-repr/shape/loci/angle.d.ts

@@ -27,14 +27,18 @@ export declare const AngleParams: {
     tether: PD.BooleanParam;
     tetherLength: PD.Numeric;
     tetherBaseWidth: PD.Numeric;
-    attachment: PD.Select<"middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right">;
+    attachment: PD.Select<"bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right">;
     fontFamily: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontFamily>;
     fontQuality: PD.Select<number>;
     fontStyle: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontStyle>;
     fontVariant: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontVariant>;
     fontWeight: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
     ignoreLight: PD.BooleanParam;
     sectorOpacity: PD.Numeric;
     color: PD.Color;

package/lib/mol-repr/shape/loci/common.d.ts

@@ -27,13 +27,17 @@ export declare const LociLabelTextParams: {
     tether: PD.BooleanParam;
     tetherLength: PD.Numeric;
     tetherBaseWidth: PD.Numeric;
-    attachment: PD.Select<"middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right">;
+    attachment: PD.Select<"bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right">;
     fontFamily: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontFamily>;
     fontQuality: PD.Select<number>;
     fontStyle: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontStyle>;
     fontVariant: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontVariant>;
     fontWeight: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type LociLabelTextParams = typeof LociLabelTextParams;

package/lib/mol-repr/shape/loci/dihedral.d.ts

@@ -27,14 +27,18 @@ export declare const DihedralParams: {
     tether: PD.BooleanParam;
     tetherLength: PD.Numeric;
     tetherBaseWidth: PD.Numeric;
-    attachment: PD.Select<"middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right">;
+    attachment: PD.Select<"bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right">;
     fontFamily: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontFamily>;
     fontQuality: PD.Select<number>;
     fontStyle: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontStyle>;
     fontVariant: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontVariant>;
     fontWeight: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
     ignoreLight: PD.BooleanParam;
     sectorOpacity: PD.Numeric;
     color: PD.Color;

package/lib/mol-repr/shape/loci/distance.d.ts

@@ -10,7 +10,7 @@ export interface DistanceData {
     pairs: Loci.Bundle<2>[];
 }
 export declare const DistanceParams: {
-    visuals: PD.MultiSelect<"lines" | "text">;
+    visuals: PD.MultiSelect<"text" | "lines">;
     unitLabel: PD.Text<string>;
     borderWidth: PD.Numeric;
     customText: PD.Text<string>;
@@ -28,14 +28,18 @@ export declare const DistanceParams: {
     tether: PD.BooleanParam;
     tetherLength: PD.Numeric;
     tetherBaseWidth: PD.Numeric;
-    attachment: PD.Select<"middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right">;
+    attachment: PD.Select<"bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right">;
     fontFamily: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontFamily>;
     fontQuality: PD.Select<number>;
     fontStyle: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontStyle>;
     fontVariant: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontVariant>;
     fontWeight: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
     lineSizeAttenuation: PD.BooleanParam;
     linesColor: PD.Color;
     linesSize: PD.Numeric;

package/lib/mol-repr/shape/loci/label.d.ts

@@ -31,14 +31,18 @@ export declare const LabelParams: {
     tether: PD.BooleanParam;
     tetherLength: PD.Numeric;
     tetherBaseWidth: PD.Numeric;
-    attachment: PD.Select<"middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right">;
+    attachment: PD.Select<"bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right">;
     fontFamily: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontFamily>;
     fontQuality: PD.Select<number>;
     fontStyle: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontStyle>;
     fontVariant: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontVariant>;
     fontWeight: PD.Select<import("../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type LabelParams = typeof LabelParams;
 export declare type LabelProps = PD.Values<LabelParams>;

package/lib/mol-repr/shape/loci/orientation.d.ts

@@ -20,7 +20,11 @@ export declare const OrientationParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type OrientationParams = typeof OrientationParams;
 export declare type OrientationProps = PD.Values<OrientationParams>;

package/lib/mol-repr/shape/loci/plane.d.ts

@@ -19,7 +19,11 @@ export declare const PlaneParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type PlaneParams = typeof PlaneParams;
 export declare type PlaneProps = PD.Values<PlaneParams>;

package/lib/mol-repr/shape/model/unitcell.d.ts

@@ -22,7 +22,11 @@ export declare const UnitcellParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>>;
 };
 export declare type UnitcellParams = typeof UnitcellParams;
 export declare type UnitcellProps = PD.Values<UnitcellParams>;

package/lib/mol-repr/shape/representation.js

@@ -31,6 +31,7 @@ export function ShapeRepresentation(getShape, geometryUtils, builder) {
     var renderObjects = [];
     var _renderObject;
     var _shape;
+    var geometryVersion = -1;
     var _theme = Theme.createEmpty();
     var currentProps = PD.getDefaultValues(geometryUtils.Params); // TODO avoid casting
     var currentParams;
@@ -151,6 +152,9 @@ export function ShapeRepresentation(getShape, geometryUtils, builder) {
                             geometryUtils.updateRenderableState(_renderObject.state, newProps);
                         }
                         currentProps = newProps;
+                        if (updateState.createGeometry || updateState.createNew) {
+                            geometryVersion += 1;
+                        }
                         // increment version
                         updated.next(version++);
                         return [2 /*return*/];
@@ -174,6 +178,7 @@ export function ShapeRepresentation(getShape, geometryUtils, builder) {
         get state() { return _state; },
         get theme() { return _theme; },
         renderObjects: renderObjects,
+        get geometryVersion() { return geometryVersion; },
         updated: updated,
         createOrUpdate: createOrUpdate,
         getLoci: function (pickingId) {
@@ -215,6 +220,9 @@ export function ShapeRepresentation(getShape, geometryUtils, builder) {
                 if (state.transparency !== undefined) {
                     Visual.setTransparency(_renderObject, state.transparency, lociApply, true);
                 }
+                if (state.substance !== undefined) {
+                    Visual.setSubstance(_renderObject, state.substance, lociApply, true);
+                }
                 if (state.transform !== undefined)
                     Visual.setTransform(_renderObject, state.transform);
             }

package/lib/mol-repr/shape/representation.js.map

@@ -1 +1 @@
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package/lib/mol-repr/structure/complex-representation.js

@@ -7,6 +7,7 @@
 import { __awaiter, __generator } from "tslib";
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { StructureRepresentationStateBuilder } from './representation';
+import { Representation } from '../representation';
 import { Structure, StructureElement, Bond } from '../../mol-model/structure';
 import { Subject } from 'rxjs';
 import { getNextMaterialId } from '../../mol-gl/render-object';
@@ -17,10 +18,12 @@ import { MarkerActions } from '../../mol-util/marker-action';
 import { Overpaint } from '../../mol-theme/overpaint';
 import { Clipping } from '../../mol-theme/clipping';
 import { Transparency } from '../../mol-theme/transparency';
+import { Substance } from '../../mol-theme/substance';
 export function ComplexRepresentation(label, ctx, getParams, visualCtor) {
     var version = 0;
     var webgl = ctx.webgl;
     var updated = new Subject();
+    var geometryState = new Representation.GeometryState();
     var materialId = getNextMaterialId();
     var renderObjects = [];
     var _state = StructureRepresentationStateBuilder.create();
@@ -66,10 +69,14 @@ export function ComplexRepresentation(label, ctx, getParams, visualCtor) {
                             setState(_state); // current state for new visual
                         // update list of renderObjects
                         renderObjects.length = 0;
-                        if (visual && visual.renderObject)
+                        if (visual && visual.renderObject) {
                             renderObjects.push(visual.renderObject);
+                            geometryState.add(visual.renderObject.id, visual.geometryVersion);
+                        }
+                        geometryState.snapshot();
                         // increment version
-                        updated.next(version++);
+                        version += 1;
+                        updated.next(version);
                         return [2 /*return*/];
                 }
             });
@@ -115,12 +122,17 @@ export function ComplexRepresentation(label, ctx, getParams, visualCtor) {
         if (state.overpaint !== undefined && visual) {
             // Remap loci from equivalent structure to the current structure
             var remappedOverpaint = Overpaint.remap(state.overpaint, _structure);
-            visual.setOverpaint(remappedOverpaint);
+            visual.setOverpaint(remappedOverpaint, webgl);
         }
         if (state.transparency !== undefined && visual) {
             // Remap loci from equivalent structure to the current structure
             var remappedTransparency = Transparency.remap(state.transparency, _structure);
-            visual.setTransparency(remappedTransparency);
+            visual.setTransparency(remappedTransparency, webgl);
+        }
+        if (state.substance !== undefined && visual) {
+            // Remap loci from equivalent structure to the current structure
+            var remappedSubstance = Substance.remap(state.substance, _structure);
+            visual.setSubstance(remappedSubstance, webgl);
         }
         if (state.clipping !== undefined && visual) {
             // Remap loci from equivalent structure to the current structure
@@ -152,6 +164,7 @@ export function ComplexRepresentation(label, ctx, getParams, visualCtor) {
         get params() { return _params; },
         get state() { return _state; },
         get theme() { return _theme; },
+        get geometryVersion() { return geometryState.version; },
         renderObjects: renderObjects,
         updated: updated,
         createOrUpdate: createOrUpdate,