molstar 3.6.0 → 3.8.0

package/lib/mol-theme/color/volume-value.js

@@ -1,12 +1,11 @@
 /**
- * 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>
  */
-import { Color, ColorScale } from '../../mol-util/color';
+import { ColorScale } from '../../mol-util/color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ColorNames } from '../../mol-util/color/names';
-var DefaultColor = Color(0xCCCCCC);
 var Description = 'Assign color based on the given value of a volume cell.';
 export var VolumeValueColorThemeParams = {
     colorList: PD.ColorList({
@@ -33,7 +32,6 @@ export function VolumeValueColorTheme(ctx, props) {
     return {
         factory: VolumeValueColorTheme,
         granularity: 'direct',
-        color: function () { return DefaultColor; },
         props: props,
         description: Description,
         legend: scale.legend,

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

@@ -1,21 +1,25 @@
 /**
- * Copyright (c) 2018-2021 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>
  */
 import { Color } from '../mol-util/color';
 import { Location } from '../mol-model/location';
-import { ColorType } from '../mol-geo/geometry/color-data';
+import { ColorType, ColorTypeDirect, ColorTypeGrid, ColorTypeLocation } from '../mol-geo/geometry/color-data';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { ThemeDataContext, ThemeRegistry, ThemeProvider } from './theme';
 import { ScaleLegend, TableLegend } from '../mol-util/legend';
-import { TextureFilter } from '../mol-gl/webgl/texture';
+import { Texture, TextureFilter } from '../mol-gl/webgl/texture';
+import { Vec3, Vec4 } from '../mol-math/linear-algebra';
 export declare type LocationColor = (location: Location, isSecondary: boolean) => Color;
+export interface ColorVolume {
+    colors: Texture;
+    dimension: Vec3;
+    transform: Vec4;
+}
 export { ColorTheme };
-interface ColorTheme<P extends PD.Params> {
-    readonly factory: ColorTheme.Factory<P>;
-    readonly granularity: ColorType;
-    readonly color: LocationColor;
+declare type ColorThemeShared<P extends PD.Params, G extends ColorType> = {
+    readonly factory: ColorTheme.Factory<P, G>;
     readonly props: Readonly<PD.Values<P>>;
     /**
      * if palette is defined, 24bit RGB color value normalized to interval [0, 1]
@@ -26,7 +30,19 @@ interface ColorTheme<P extends PD.Params> {
     readonly contextHash?: number;
     readonly description?: string;
     readonly legend?: Readonly<ScaleLegend | TableLegend>;
-}
+};
+declare type ColorThemeLocation<P extends PD.Params> = {
+    readonly granularity: ColorTypeLocation;
+    readonly color: LocationColor;
+} & ColorThemeShared<P, ColorTypeLocation>;
+declare type ColorThemeGrid<P extends PD.Params> = {
+    readonly granularity: ColorTypeGrid;
+    readonly grid: ColorVolume;
+} & ColorThemeShared<P, ColorTypeGrid>;
+declare type ColorThemeDirect<P extends PD.Params> = {
+    readonly granularity: ColorTypeDirect;
+} & ColorThemeShared<P, ColorTypeDirect>;
+declare type ColorTheme<P extends PD.Params, G extends ColorType = ColorTypeLocation> = G extends ColorTypeLocation ? ColorThemeLocation<P> : G extends ColorTypeGrid ? ColorThemeGrid<P> : G extends ColorTypeDirect ? ColorThemeDirect<P> : never;
 declare namespace ColorTheme {
     export const enum Category {
         Atom = "Atom Property",
@@ -44,15 +60,15 @@ declare namespace ColorTheme {
     export type Props = {
         [k: string]: any;
     };
-    export type Factory<P extends PD.Params> = (ctx: ThemeDataContext, props: PD.Values<P>) => ColorTheme<P>;
-    export const EmptyFactory: () => ColorTheme<{}>;
+    export type Factory<P extends PD.Params, G extends ColorType> = (ctx: ThemeDataContext, props: PD.Values<P>) => ColorTheme<P, G>;
+    export const EmptyFactory: () => ColorThemeLocation<{}>;
     export const Empty: ColorTheme<{}>;
-    export function areEqual(themeA: ColorTheme<any>, themeB: ColorTheme<any>): boolean;
-    export interface Provider<P extends PD.Params = any, Id extends string = string> extends ThemeProvider<ColorTheme<P>, P, Id> {
+    export function areEqual(themeA: ColorTheme<any, any>, themeB: ColorTheme<any, any>): boolean;
+    export interface Provider<P extends PD.Params = any, Id extends string = string, G extends ColorType = ColorType> extends ThemeProvider<ColorTheme<P, G>, P, Id, G> {
     }
     export const EmptyProvider: Provider<{}>;
-    export type Registry = ThemeRegistry<ColorTheme<any>>;
-    export function createRegistry(): ThemeRegistry<ColorTheme<{}>>;
+    export type Registry = ThemeRegistry<ColorTheme<any, any>>;
+    export function createRegistry(): ThemeRegistry<ColorThemeLocation<{}> | ColorThemeDirect<{}> | ColorThemeGrid<{}>>;
     export const BuiltIn: {
         'atom-id': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
@@ -68,8 +84,8 @@ declare namespace ColorTheme {
                     colors: import("../mol-util/color/color").ColorListEntry[];
                 };
             }>, "colors">>;
-        }, "atom-id">;
-        'carbohydrate-symbol': Provider<{}, "carbohydrate-symbol">;
+        }, "atom-id", ColorType>;
+        'carbohydrate-symbol': Provider<{}, "carbohydrate-symbol", ColorType>;
         'chain-id': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 maxCount: number;
@@ -85,7 +101,7 @@ declare namespace ColorTheme {
                 };
             }>, "colors">>;
             asymId: PD.Select<"label" | "auth">;
-        }, "chain-id">;
+        }, "chain-id", ColorType>;
         'element-index': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 maxCount: number;
@@ -100,7 +116,7 @@ declare namespace ColorTheme {
                     colors: import("../mol-util/color/color").ColorListEntry[];
                 };
             }>, "colors">>;
-        }, "element-index">;
+        }, "element-index", ColorType>;
         'element-symbol': Provider<{
             carbonColor: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "element-symbol"> | PD.NamedParams<PD.Normalize<{
                 palette: PD.NamedParams<PD.Normalize<{
@@ -271,7 +287,7 @@ declare namespace ColorTheme {
                 LV: Color;
                 UUH: Color;
             }>, "custom">>;
-        }, "element-symbol">;
+        }, "element-symbol", ColorType>;
         'entity-id': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 maxCount: number;
@@ -286,7 +302,7 @@ declare namespace ColorTheme {
                     colors: import("../mol-util/color/color").ColorListEntry[];
                 };
             }>, "colors">>;
-        }, "entity-id">;
+        }, "entity-id", ColorType>;
         'entity-source': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 maxCount: number;
@@ -301,11 +317,11 @@ declare namespace ColorTheme {
                     colors: import("../mol-util/color/color").ColorListEntry[];
                 };
             }>, "colors">>;
-        }, "entity-source">;
+        }, "entity-source", ColorType>;
         hydrophobicity: Provider<{
             list: PD.ColorList;
             scale: PD.Select<"DGwif" | "DGwoct" | "Oct-IF">;
-        }, "hydrophobicity">;
+        }, "hydrophobicity", ColorType>;
         illustrative: Provider<{
             style: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 palette: PD.NamedParams<PD.Normalize<{
@@ -357,7 +373,7 @@ declare namespace ColorTheme {
                 }>, "custom">;
             }>, "molecule-type">>;
             carbonLightness: PD.Numeric;
-        }, "illustrative">;
+        }, "illustrative", ColorType>;
         'model-index': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 maxCount: number;
@@ -372,7 +388,7 @@ declare namespace ColorTheme {
                     colors: import("../mol-util/color/color").ColorListEntry[];
                 };
             }>, "colors">>;
-        }, "model-index">;
+        }, "model-index", ColorType>;
         'molecule-type': Provider<{
             saturation: PD.Numeric;
             lightness: PD.Numeric;
@@ -385,11 +401,11 @@ declare namespace ColorTheme {
                 PNA: Color;
                 saccharide: Color;
             }>, "custom">>;
-        }, "molecule-type">;
+        }, "molecule-type", ColorType>;
         occupancy: Provider<{
             domain: PD.Interval;
             list: PD.ColorList;
-        }, "occupancy">;
+        }, "occupancy", ColorType>;
         'operator-hkl': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 maxCount: number;
@@ -404,7 +420,7 @@ declare namespace ColorTheme {
                     colors: import("../mol-util/color/color").ColorListEntry[];
                 };
             }>, "colors">>;
-        }, "operator-hkl">;
+        }, "operator-hkl", ColorType>;
         'operator-name': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 maxCount: number;
@@ -419,11 +435,11 @@ declare namespace ColorTheme {
                     colors: import("../mol-util/color/color").ColorListEntry[];
                 };
             }>, "colors">>;
-        }, "operator-name">;
+        }, "operator-name", ColorType>;
         'partial-charge': Provider<{
             domain: PD.Interval;
             list: PD.ColorList;
-        }, "partial-charge">;
+        }, "partial-charge", ColorType>;
         'polymer-id': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 maxCount: number;
@@ -438,7 +454,7 @@ declare namespace ColorTheme {
                     colors: import("../mol-util/color/color").ColorListEntry[];
                 };
             }>, "colors">>;
-        }, "polymer-id">;
+        }, "polymer-id", ColorType>;
         'polymer-index': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 maxCount: number;
@@ -453,7 +469,7 @@ declare namespace ColorTheme {
                     colors: import("../mol-util/color/color").ColorListEntry[];
                 };
             }>, "colors">>;
-        }, "polymer-index">;
+        }, "polymer-index", ColorType>;
         'residue-name': Provider<{
             saturation: PD.Numeric;
             lightness: PD.Numeric;
@@ -495,7 +511,7 @@ declare namespace ColorTheme {
                 CPN: Color;
                 TPN: Color;
             }>, "custom">>;
-        }, "residue-name">;
+        }, "residue-name", ColorType>;
         'secondary-structure': Provider<{
             saturation: PD.Numeric;
             lightness: PD.Numeric;
@@ -512,15 +528,15 @@ declare namespace ColorTheme {
                 rna: Color;
                 carbohydrate: Color;
             }>, "custom">>;
-        }, "secondary-structure">;
+        }, "secondary-structure", ColorType>;
         'sequence-id': Provider<{
             list: PD.ColorList;
-        }, "sequence-id">;
-        'shape-group': Provider<{}, "shape-group">;
+        }, "sequence-id", ColorType>;
+        'shape-group': Provider<{}, "shape-group", ColorType>;
         uncertainty: Provider<{
             domain: PD.Interval;
             list: PD.ColorList;
-        }, "uncertainty">;
+        }, "uncertainty", ColorType>;
         'unit-index': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 maxCount: number;
@@ -535,13 +551,13 @@ declare namespace ColorTheme {
                     colors: import("../mol-util/color/color").ColorListEntry[];
                 };
             }>, "colors">>;
-        }, "unit-index">;
+        }, "unit-index", ColorType>;
         uniform: Provider<{
             value: PD.Color;
-        }, "uniform">;
+        }, "uniform", ColorType>;
         'volume-value': Provider<{
             colorList: PD.ColorList;
-        }, "volume-value">;
+        }, "volume-value", ColorType>;
     };
     type _BuiltIn = typeof BuiltIn;
     export type BuiltIn = keyof _BuiltIn;

package/lib/mol-theme/color.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 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>
  */

package/lib/mol-theme/theme.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>
  */
@@ -10,6 +10,7 @@ import { Volume } from '../mol-model/volume';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { Shape } from '../mol-model/shape';
 import { CustomProperty } from '../mol-model-props/common/custom-property';
+import { ColorType } from '../mol-geo/geometry/color-data';
 export interface ThemeRegistryContext {
     colorThemeRegistry: ColorTheme.Registry;
     sizeThemeRegistry: SizeTheme.Registry;
@@ -22,7 +23,7 @@ export interface ThemeDataContext {
 }
 export { Theme };
 interface Theme {
-    color: ColorTheme<any>;
+    color: ColorTheme<any, any>;
     size: SizeTheme<any>;
 }
 declare namespace Theme {
@@ -35,7 +36,7 @@ declare namespace Theme {
     export function releaseDependencies(theme: ThemeRegistryContext, data: ThemeDataContext, props: Props): void;
     export {};
 }
-export interface ThemeProvider<T extends ColorTheme<P> | SizeTheme<P>, P extends PD.Params, Id extends string = string> {
+export interface ThemeProvider<T extends ColorTheme<P, G> | SizeTheme<P>, P extends PD.Params, Id extends string = string, G extends ColorType = ColorType> {
     readonly name: Id;
     readonly label: string;
     readonly category: string;
@@ -48,18 +49,18 @@ export interface ThemeProvider<T extends ColorTheme<P> | SizeTheme<P>, P extends
         detach: (data: ThemeDataContext) => void;
     };
 }
-export declare class ThemeRegistry<T extends ColorTheme<any> | SizeTheme<any>> {
+export declare class ThemeRegistry<T extends ColorTheme<any, any> | SizeTheme<any>> {
     private emptyProvider;
     private _list;
     private _map;
     private _name;
     get default(): {
         name: string;
-        provider: ThemeProvider<T, any, string>;
+        provider: ThemeProvider<T, any, string, ColorType>;
     };
     get list(): {
         name: string;
-        provider: ThemeProvider<T, any, string>;
+        provider: ThemeProvider<T, any, string, ColorType>;
     }[];
     get types(): [string, string, string][];
     constructor(builtInThemes: {
@@ -74,7 +75,7 @@ export declare class ThemeRegistry<T extends ColorTheme<any> | SizeTheme<any>> {
     create(name: string, ctx: ThemeDataContext, props?: {}): T;
     getApplicableList(ctx: ThemeDataContext): {
         name: string;
-        provider: ThemeProvider<T, any, string>;
+        provider: ThemeProvider<T, any, string, ColorType>;
     }[];
     getApplicableTypes(ctx: ThemeDataContext): [string, string, string][];
 }

package/lib/mol-theme/theme.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>
  */

package/lib/servers/model/server/query.js

@@ -256,10 +256,8 @@ function resolveJobEntry(entry, structure, encoder) {
                     encoder.writeCategory(_model_server_result, entry);
                     encoder.writeCategory(_model_server_params, entry);
                     if (entry.queryDefinition.niceName === 'Ligand') {
-                        if (encoder instanceof MolEncoder) {
-                            encoder.setComponentAtomData(ComponentAtom.Provider.get(structure.models[0]));
-                        }
                         if (encoder instanceof MolEncoder || encoder instanceof Mol2Encoder) {
+                            encoder.setComponentAtomData(ComponentAtom.Provider.get(structure.models[0]));
                             encoder.setComponentBondData(ComponentBond.Provider.get(structure.models[0]));
                         }
                     }

package/lib/servers/model/version.d.ts

@@ -3,4 +3,4 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
-export declare const VERSION = "0.9.8";
+export declare const VERSION = "0.9.9";

package/lib/servers/model/version.js

@@ -3,4 +3,4 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
-export var VERSION = '0.9.8';
+export var VERSION = '0.9.9';