molstar 3.0.0-dev.6 → 3.0.0

package/lib/mol-repr/volume/slice.d.ts

@@ -65,6 +65,16 @@ export declare const SliceParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type SliceParams = typeof SliceParams;
 export declare function getSliceParams(ctx: ThemeRegistryContext, volume: Volume): {
@@ -121,6 +131,16 @@ export declare function getSliceParams(ctx: ThemeRegistryContext, volume: Volume
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare function SliceVisual(materialId: number): VolumeVisual<SliceParams>;
 export declare function SliceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, SliceParams>): VolumeRepresentation<SliceParams>;
@@ -178,4 +198,14 @@ export declare const SliceRepresentationProvider: VolumeRepresentationProvider<{
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, "slice">;

package/lib/mol-repr/volume/slice.js

@@ -15,7 +15,7 @@ import { Interval, SortedArray } from '../../mol-data/int';
 import { transformPositionArray } from '../../mol-geo/util';
 import { Color } from '../../mol-util/color';
 import { ColorTheme } from '../../mol-theme/color';
-import { encodeFloatRGBtoArray } from '../../mol-util/float-packing';
+import { packIntToRGBArray } from '../../mol-util/number-packing';
 import { eachVolumeLoci } from './util';
 export function createImage(ctx, volume, theme, props, image) {
     return __awaiter(this, void 0, void 0, function () {
@@ -99,7 +99,7 @@ function getPackedGroupArray(grid, props) {
     for (var iy = y0; iy < ny; ++iy) {
         for (var ix = x0; ix < nx; ++ix) {
             for (var iz = z0; iz < nz; ++iz) {
-                encodeFloatRGBtoArray(space.dataOffset(ix, iy, iz), groupArray, j);
+                packIntToRGBArray(space.dataOffset(ix, iy, iz), groupArray, j);
                 j += 4;
             }
         }

package/lib/mol-repr/volume/util.js

@@ -7,7 +7,7 @@ import { Volume } from '../../mol-model/volume';
 import { Interval, OrderedSet } from '../../mol-data/int';
 import { equalEps } from '../../mol-math/linear-algebra/3d/common';
 import { Vec3 } from '../../mol-math/linear-algebra/3d/vec3';
-import { encodeFloatRGBtoArray } from '../../mol-util/float-packing';
+import { packIntToRGBArray } from '../../mol-util/number-packing';
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 var v3set = Vec3.set;
 var v3normalize = Vec3.normalize;
@@ -113,7 +113,7 @@ export function createVolumeTexture2d(volume, variant, padding) {
                 }
                 else {
                     if (variant === 'groups') {
-                        encodeFloatRGBtoArray(offset, array, index);
+                        packIntToRGBArray(offset, array, index);
                     }
                     else {
                         v3set(n0, data[o(Math.max(0, x - 1), y, z)], data[o(x, Math.max(0, y - 1), z)], data[o(x, y, Math.max(0, z - 1))]);

package/lib/mol-state/tree/immutable.d.ts

@@ -29,11 +29,23 @@ declare namespace StateTree {
         readonly map: OrderedSet<Ref>['map'];
         toArray(): Ref[];
         first(): Ref;
+        asMutable(): MutableChildSet;
+    }
+    export interface MutableChildSet extends ChildSet {
+        add(ref: Ref): MutableChildSet;
+        remove(ref: Ref): MutableChildSet;
+        asImmutable(): ChildSet;
     }
     interface _Map<T> {
         readonly size: number;
         has(ref: Ref): boolean;
         get(ref: Ref): T;
+        asImmutable(): _Map<T>;
+        asMutable(): MutableMap<T>;
+    }
+    export interface MutableMap<T> extends _Map<T> {
+        set(ref: Ref, value: T): MutableMap<T>;
+        delete(ref: Ref): MutableMap<T>;
     }
     export interface Transforms extends _Map<StateTransform> {
     }
@@ -41,6 +53,12 @@ declare namespace StateTree {
     }
     export interface Dependencies extends _Map<ChildSet> {
     }
+    export interface MutableTransforms extends MutableMap<StateTransform> {
+    }
+    export interface MutableChildren extends MutableMap<MutableChildSet> {
+    }
+    export interface MutableDependencies extends MutableMap<MutableChildSet> {
+    }
     /**
      * Create an instance of an immutable tree.
      */

package/lib/mol-state/tree/transient.d.ts

@@ -3,15 +3,14 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
-import { Map as ImmutableMap, OrderedSet } from 'immutable';
 import { StateTransform } from '../transform';
 import { StateTree } from './immutable';
 export { TransientTree };
 declare class TransientTree implements StateTree {
     private tree;
-    transforms: ImmutableMap<string, StateTransform<import("../transformer").StateTransformer<import("../object").StateObject<any, import("../object").StateObject.Type<any>>, import("../object").StateObject<any, import("../object").StateObject.Type<any>>, any>>>;
-    children: ImmutableMap<string, OrderedSet<string>>;
-    dependencies: ImmutableMap<string, OrderedSet<string>>;
+    transforms: StateTree.MutableTransforms;
+    children: StateTree.MutableChildren;
+    dependencies: StateTree.MutableDependencies;
     private changedNodes;
     private changedChildren;
     private changedDependencies;

package/lib/mol-theme/clipping.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,7 +10,7 @@ export { Clipping };
 declare type Clipping = {
     readonly layers: ReadonlyArray<Clipping.Layer>;
 };
-declare function Clipping(layers: ReadonlyArray<Clipping.Layer>): Clipping;
+declare function Clipping(layers: Clipping['layers']): Clipping;
 declare namespace Clipping {
     type Layer = {
         readonly loci: StructureElement.Loci;
@@ -44,22 +44,14 @@ declare namespace Clipping {
         function fromNames(names: Names[]): Flag;
         function toNames(groups: Groups): Names[];
     }
-    /** Clip object types */
-    const Type: {
-        none: number;
-        plane: number;
-        sphere: number;
-        cube: number;
-        cylinder: number;
-        infiniteCone: number;
-    };
-    type Variant = 'instance' | 'pixel';
     function areEqual(cA: Clipping, cB: Clipping): boolean;
+    /** Check if layers empty */
     function isEmpty(clipping: Clipping): boolean;
-    function remap(clipping: Clipping, structure: Structure): {
-        layers: Layer[];
-    };
+    /** Remap layers */
+    function remap(clipping: Clipping, structure: Structure): Clipping;
+    /** Merge layers */
     function merge(clipping: Clipping): Clipping;
+    /** Filter layers */
     function filter(clipping: Clipping, filter: Structure): Clipping;
     type ScriptLayer = {
         script: Script;

package/lib/mol-theme/clipping.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -69,18 +69,7 @@ function Clipping(layers) {
         }
         Groups.toNames = toNames;
     })(Groups = Clipping.Groups || (Clipping.Groups = {}));
-    /** Clip object types */
-    Clipping.Type = {
-        none: 0,
-        plane: 1,
-        sphere: 2,
-        cube: 3,
-        cylinder: 4,
-        infiniteCone: 5,
-    };
     function areEqual(cA, cB) {
-        if (cA.layers.length === 0 && cB.layers.length === 0)
-            return true;
         if (cA.layers.length !== cB.layers.length)
             return false;
         for (var i = 0, il = cA.layers.length; i < il; ++i) {
@@ -92,10 +81,12 @@ function Clipping(layers) {
         return true;
     }
     Clipping.areEqual = areEqual;
+    /** Check if layers empty */
     function isEmpty(clipping) {
         return clipping.layers.length === 0;
     }
     Clipping.isEmpty = isEmpty;
+    /** Remap layers */
     function remap(clipping, structure) {
         var layers = [];
         for (var _i = 0, _a = clipping.layers; _i < _a.length; _i++) {
@@ -109,6 +100,7 @@ function Clipping(layers) {
         return { layers: layers };
     }
     Clipping.remap = remap;
+    /** Merge layers */
     function merge(clipping) {
         if (isEmpty(clipping))
             return clipping;
@@ -133,6 +125,7 @@ function Clipping(layers) {
         return { layers: layers };
     }
     Clipping.merge = merge;
+    /** Filter layers */
     function filter(clipping, filter) {
         if (isEmpty(clipping))
             return clipping;

package/lib/mol-theme/color/element-symbol.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -157,6 +157,127 @@ export declare const ElementSymbolColorThemeParams: {
     }>, "operator-name">>;
     saturation: PD.Numeric;
     lightness: PD.Numeric;
+    colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+        H: Color;
+        D: Color;
+        T: Color;
+        HE: Color;
+        LI: Color;
+        BE: Color;
+        B: Color;
+        C: Color;
+        N: Color;
+        O: Color;
+        F: Color;
+        NE: Color;
+        NA: Color;
+        MG: Color;
+        AL: Color;
+        SI: Color;
+        P: Color;
+        S: Color;
+        CL: Color;
+        AR: Color;
+        K: Color;
+        CA: Color;
+        SC: Color;
+        TI: Color;
+        V: Color;
+        CR: Color;
+        MN: Color;
+        FE: Color;
+        CO: Color;
+        NI: Color;
+        CU: Color;
+        ZN: Color;
+        GA: Color;
+        GE: Color;
+        AS: Color;
+        SE: Color;
+        BR: Color;
+        KR: Color;
+        RB: Color;
+        SR: Color;
+        Y: Color;
+        ZR: Color;
+        NB: Color;
+        MO: Color;
+        TC: Color;
+        RU: Color;
+        RH: Color;
+        PD: Color;
+        AG: Color;
+        CD: Color;
+        IN: Color;
+        SN: Color;
+        SB: Color;
+        TE: Color;
+        I: Color;
+        XE: Color;
+        CS: Color;
+        BA: Color;
+        LA: Color;
+        CE: Color;
+        PR: Color;
+        ND: Color;
+        PM: Color;
+        SM: Color;
+        EU: Color;
+        GD: Color;
+        TB: Color;
+        DY: Color;
+        HO: Color;
+        ER: Color;
+        TM: Color;
+        YB: Color;
+        LU: Color;
+        HF: Color;
+        TA: Color;
+        W: Color;
+        RE: Color;
+        OS: Color;
+        IR: Color;
+        PT: Color;
+        AU: Color;
+        HG: Color;
+        TL: Color;
+        PB: Color;
+        BI: Color;
+        PO: Color;
+        AT: Color;
+        RN: Color;
+        FR: Color;
+        RA: Color;
+        AC: Color;
+        TH: Color;
+        PA: Color;
+        U: Color;
+        NP: Color;
+        PU: Color;
+        AM: Color;
+        CM: Color;
+        BK: Color;
+        CF: Color;
+        ES: Color;
+        FM: Color;
+        MD: Color;
+        NO: Color;
+        LR: Color;
+        RF: Color;
+        DB: Color;
+        SG: Color;
+        BH: Color;
+        HS: Color;
+        MT: Color;
+        DS: Color;
+        RG: Color;
+        CN: Color;
+        UUT: Color;
+        FL: Color;
+        UUP: Color;
+        LV: Color;
+        UUH: Color;
+    }>, "custom">>;
 };
 export declare type ElementSymbolColorThemeParams = typeof ElementSymbolColorThemeParams;
 export declare function getElementSymbolColorThemeParams(ctx: ThemeDataContext): {
@@ -186,6 +307,127 @@ export declare function getElementSymbolColorThemeParams(ctx: ThemeDataContext):
     }>, "operator-name">>;
     saturation: PD.Numeric;
     lightness: PD.Numeric;
+    colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+        H: Color;
+        D: Color;
+        T: Color;
+        HE: Color;
+        LI: Color;
+        BE: Color;
+        B: Color;
+        C: Color;
+        N: Color;
+        O: Color;
+        F: Color;
+        NE: Color;
+        NA: Color;
+        MG: Color;
+        AL: Color;
+        SI: Color;
+        P: Color;
+        S: Color;
+        CL: Color;
+        AR: Color;
+        K: Color;
+        CA: Color;
+        SC: Color;
+        TI: Color;
+        V: Color;
+        CR: Color;
+        MN: Color;
+        FE: Color;
+        CO: Color;
+        NI: Color;
+        CU: Color;
+        ZN: Color;
+        GA: Color;
+        GE: Color;
+        AS: Color;
+        SE: Color;
+        BR: Color;
+        KR: Color;
+        RB: Color;
+        SR: Color;
+        Y: Color;
+        ZR: Color;
+        NB: Color;
+        MO: Color;
+        TC: Color;
+        RU: Color;
+        RH: Color;
+        PD: Color;
+        AG: Color;
+        CD: Color;
+        IN: Color;
+        SN: Color;
+        SB: Color;
+        TE: Color;
+        I: Color;
+        XE: Color;
+        CS: Color;
+        BA: Color;
+        LA: Color;
+        CE: Color;
+        PR: Color;
+        ND: Color;
+        PM: Color;
+        SM: Color;
+        EU: Color;
+        GD: Color;
+        TB: Color;
+        DY: Color;
+        HO: Color;
+        ER: Color;
+        TM: Color;
+        YB: Color;
+        LU: Color;
+        HF: Color;
+        TA: Color;
+        W: Color;
+        RE: Color;
+        OS: Color;
+        IR: Color;
+        PT: Color;
+        AU: Color;
+        HG: Color;
+        TL: Color;
+        PB: Color;
+        BI: Color;
+        PO: Color;
+        AT: Color;
+        RN: Color;
+        FR: Color;
+        RA: Color;
+        AC: Color;
+        TH: Color;
+        PA: Color;
+        U: Color;
+        NP: Color;
+        PU: Color;
+        AM: Color;
+        CM: Color;
+        BK: Color;
+        CF: Color;
+        ES: Color;
+        FM: Color;
+        MD: Color;
+        NO: Color;
+        LR: Color;
+        RF: Color;
+        DB: Color;
+        SG: Color;
+        BH: Color;
+        HS: Color;
+        MT: Color;
+        DS: Color;
+        RG: Color;
+        CN: Color;
+        UUT: Color;
+        FL: Color;
+        UUP: Color;
+        LV: Color;
+        UUH: Color;
+    }>, "custom">>;
 };
 export declare function elementSymbolColor(colorMap: ElementSymbolColors, element: ElementSymbol): Color;
 export declare function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<ElementSymbolColorThemeParams>): ColorTheme<ElementSymbolColorThemeParams>;

package/lib/mol-theme/color/element-symbol.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,6 +9,7 @@ import { StructureElement, Unit, Bond } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { TableLegend } from '../../mol-util/legend';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
 import { ChainIdColorTheme, ChainIdColorThemeParams } from './chain-id';
 import { OperatorNameColorThemeParams, OperatorNameColorTheme } from './operator-name';
 // from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
@@ -25,7 +26,11 @@ export var ElementSymbolColorThemeParams = {
         'element-symbol': PD.Group({})
     }, { description: 'Use chain-id coloring for carbon atoms.' }),
     saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(0.2, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(0.2, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(ElementSymbolColors))
+    })
 };
 export function getElementSymbolColorThemeParams(ctx) {
     return ElementSymbolColorThemeParams; // TODO return copy
@@ -35,7 +40,7 @@ export function elementSymbolColor(colorMap, element) {
     return c === undefined ? DefaultElementSymbolColor : c;
 }
 export function ElementSymbolColorTheme(ctx, props) {
-    var colorMap = getAdjustedColorMap(ElementSymbolColors, props.saturation, props.lightness);
+    var colorMap = getAdjustedColorMap(props.colors.name === 'default' ? ElementSymbolColors : props.colors.params, props.saturation, props.lightness);
     var carbonColor = props.carbonColor.name === 'chain-id'
         ? ChainIdColorTheme(ctx, props.carbonColor.params).color
         : props.carbonColor.name === 'operator-name'
@@ -70,8 +75,8 @@ export function ElementSymbolColorTheme(ctx, props) {
         color: color,
         props: props,
         description: Description,
-        legend: TableLegend(Object.keys(ElementSymbolColors).map(function (name) {
-            return [name, ElementSymbolColors[name]];
+        legend: TableLegend(Object.keys(colorMap).map(function (name) {
+            return [name, colorMap[name]];
         }))
     };
 }

package/lib/mol-theme/color/entity-id.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-theme/color/entity-id.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -28,9 +28,30 @@ function getEntityIdSerialMap(structure) {
             if (!map.has(k))
                 map.set(k, map.size);
         }
+        var spheres_entity_id = structure.models[i].coarseHierarchy.spheres.entity_id;
+        for (var j = 0, jl = spheres_entity_id.rowCount; j < jl; ++j) {
+            var k = key(spheres_entity_id.value(j), i);
+            if (!map.has(k))
+                map.set(k, map.size);
+        }
+        var gaussians_entity_id = structure.models[i].coarseHierarchy.gaussians.entity_id;
+        for (var j = 0, jl = gaussians_entity_id.rowCount; j < jl; ++j) {
+            var k = key(gaussians_entity_id.value(j), i);
+            if (!map.has(k))
+                map.set(k, map.size);
+        }
     }
     return map;
 }
+function getEntityId(location) {
+    switch (location.unit.kind) {
+        case 0 /* Atomic */:
+            return StructureProperties.chain.label_entity_id(location);
+        case 1 /* Spheres */:
+        case 2 /* Gaussians */:
+            return StructureProperties.coarse.entity_id(location);
+    }
+}
 export function EntityIdColorTheme(ctx, props) {
     var color;
     var legend;
@@ -44,17 +65,17 @@ export function EntityIdColorTheme(ctx, props) {
         color = function (location) {
             var serial = undefined;
             if (StructureElement.Location.is(location)) {
-                var atomId = StructureProperties.chain.label_entity_id(location);
+                var entityId = getEntityId(location);
                 var modelIndex = location.structure.models.indexOf(location.unit.model);
-                var k = key(atomId, modelIndex);
+                var k = key(entityId, modelIndex);
                 serial = entityIdSerialMap_1.get(k);
             }
             else if (Bond.isLocation(location)) {
                 l_1.unit = location.aUnit;
                 l_1.element = location.aUnit.elements[location.aIndex];
-                var atomId = StructureProperties.chain.label_entity_id(l_1);
+                var entityId = getEntityId(l_1);
                 var modelIndex = l_1.structure.models.indexOf(l_1.unit.model);
-                var k = key(atomId, modelIndex);
+                var k = key(entityId, modelIndex);
                 serial = entityIdSerialMap_1.get(k);
             }
             return serial === undefined ? DefaultColor : palette_1.color(serial);