molstar 4.3.0 → 4.4.1

package/lib/commonjs/apps/mesoscale-explorer/data/state.d.ts

@@ -19,6 +19,7 @@ export declare function getDistinctGroupColors(count: number, color: Color, vari
 export declare function getDistinctBaseColors(count: number, shift: number, props?: Partial<DistinctColorsProps>): Color[];
 export declare const ColorParams: {
     type: PD.Select<string>;
+    illustrative: PD.BooleanParam;
     value: PD.Color;
     variability: PD.Numeric;
     shift: PD.Numeric;
@@ -30,6 +31,7 @@ export type ColorProps = PD.Values<typeof ColorParams>;
 export declare const ColorValueParam: PD.Color;
 export declare const RootParams: {
     type: PD.Select<string>;
+    illustrative: PD.BooleanParam;
     value: PD.Color;
     variability: PD.Numeric;
     shift: PD.Numeric;
@@ -41,16 +43,32 @@ export declare const LightnessParams: {
     lightness: PD.Numeric;
 };
 export declare const DimLightness = 6;
+export declare const IllustrativeParams: {
+    illustrative: PD.BooleanParam;
+};
 export declare const OpacityParams: {
     alpha: PD.Numeric;
 };
 export declare const EmissiveParams: {
     emissive: PD.Numeric;
 };
+export declare const celShaded: {
+    celShaded: PD.BooleanParam;
+};
+export type celShadedProps = PD.Values<typeof celShaded>;
 export declare const PatternParams: {
     frequency: PD.Numeric;
     amplitude: PD.Numeric;
 };
+export declare const StyleParams: {
+    ignoreLight: PD.BooleanParam;
+    materialStyle: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    celShaded: PD.BooleanParam;
+};
 export declare const LodParams: {
     lodLevels: PD.ObjectList<PD.Normalize<{
         minDistance: number;
@@ -119,9 +137,11 @@ export declare const MesoscaleGroupParams: {
     index: PD.Value<number>;
     tag: PD.Value<string>;
     label: PD.Value<string>;
+    description: PD.Value<string>;
     hidden: PD.BooleanParam;
     color: PD.Group<PD.Normalize<{
         type: string;
+        illustrative: boolean;
         value: Color;
         variability: number;
         shift: number;
@@ -167,16 +187,16 @@ export type MesoscaleGroupProps = PD.Values<typeof MesoscaleGroupParams>;
 declare const MesoscaleGroupObject_base: {
     new (data: {}, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../../mol-util").UUID;
         type: PSO.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: {};
     };
     type: PSO.TypeInfo;
-    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<{}, PSO.TypeInfo>;
+    is(obj?: import("../../../mol-state").StateObject): obj is import("../../../mol-state").StateObject<{}, PSO.TypeInfo>;
 };
 export declare class MesoscaleGroupObject extends MesoscaleGroupObject_base {
 }
@@ -185,9 +205,11 @@ export declare const MesoscaleGroup: import("../../../mol-state").StateTransform
     index: number;
     tag: string;
     label: string;
+    description: string;
     hidden: boolean;
     color: PD.Normalize<{
         type: any;
+        illustrative: any;
         value: any;
         variability: any;
         shift: any;
@@ -232,35 +254,47 @@ export declare const MesoscaleStateParams: {
     filter: PD.Value<string>;
     graphics: PD.Select<GraphicsMode>;
     description: PD.Value<string>;
+    focusInfo: PD.Value<string>;
     link: PD.Value<string>;
+    textSizeDescription: PD.Numeric;
+    index: PD.Value<number>;
 };
 declare const MesoscaleStateObject_base: {
     new (data: PD.Values<{
         filter: PD.Value<string>;
         graphics: PD.Select<GraphicsMode>;
         description: PD.Value<string>;
+        focusInfo: PD.Value<string>;
         link: PD.Value<string>;
+        textSizeDescription: PD.Numeric;
+        index: PD.Value<number>;
     }>, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../../mol-util").UUID;
         type: PSO.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: PD.Values<{
             filter: PD.Value<string>;
             graphics: PD.Select<GraphicsMode>;
             description: PD.Value<string>;
+            focusInfo: PD.Value<string>;
             link: PD.Value<string>;
+            textSizeDescription: PD.Numeric;
+            index: PD.Value<number>;
         }>;
     };
     type: PSO.TypeInfo;
-    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<PD.Values<{
+    is(obj?: import("../../../mol-state").StateObject): obj is import("../../../mol-state").StateObject<PD.Values<{
         filter: PD.Value<string>;
         graphics: PD.Select<GraphicsMode>;
         description: PD.Value<string>;
+        focusInfo: PD.Value<string>;
         link: PD.Value<string>;
+        textSizeDescription: PD.Numeric;
+        index: PD.Value<number>;
     }>, PSO.TypeInfo>;
 };
 export declare class MesoscaleStateObject extends MesoscaleStateObject_base {
@@ -277,12 +311,16 @@ declare const MesoscaleState: {
 export declare function getRoots(plugin: PluginContext): StateSelection.CellSeq<StateObjectCell<MesoscaleGroupObject>>;
 export declare function getGroups(plugin: PluginContext, tag?: string): StateSelection.CellSeq<StateObjectCell<MesoscaleGroupObject>>;
 export declare function getAllGroups(plugin: PluginContext, tag?: string): StateObjectCell<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateTransform<import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>[];
-export declare function getAllLeafGroups(plugin: PluginContext, tag: string): StateObjectCell<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateTransform<import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>[];
+export declare function getAllLeafGroups(plugin: PluginContext, tag: string | undefined): StateObjectCell<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateTransform<import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>[];
 type EntityCells = StateSelection.CellSeq<StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D>>;
 export declare function getEntities(plugin: PluginContext, tag?: string): EntityCells;
-export declare function getFilteredEntities(plugin: PluginContext, tag: string, filter: string): StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D, import("../../../mol-state").StateTransform<import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>[];
+export declare function getFilteredEntities(plugin: PluginContext, tag: string | undefined, filter: string | undefined): EntityCells;
 export declare function getAllEntities(plugin: PluginContext, tag?: string): EntityCells;
-export declare function getAllFilteredEntities(plugin: PluginContext, tag: string, filter: string): StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D, import("../../../mol-state").StateTransform<import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>[];
+export declare function getAllFilteredEntities(plugin: PluginContext, tag: string | undefined, filter: string | undefined): EntityCells;
+export declare function getEveryEntity(plugin: PluginContext, filter?: string, tag?: string): EntityCells;
 export declare function getEntityLabel(plugin: PluginContext, cell: StateObjectCell): string;
-export declare function updateColors(plugin: PluginContext, values: PD.Values, tag: string, filter: string): Promise<void>;
+export declare function getCellDescription(cell: StateObjectCell): string;
+export declare function getEntityDescription(plugin: PluginContext, cell: StateObjectCell): string;
+export declare function updateColors(plugin: PluginContext, values: PD.Values, options?: PD.Values, tag?: string, filter?: string): Promise<void>;
 export declare function expandAllGroups(plugin: PluginContext): void;
+export declare function updateReprParams(plugin: PluginContext, options: PD.Values): Promise<void>;

package/lib/commonjs/apps/mesoscale-explorer/data/state.js

@@ -5,7 +5,30 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.expandAllGroups = exports.updateColors = exports.getEntityLabel = exports.getAllFilteredEntities = exports.getAllEntities = exports.getFilteredEntities = exports.getEntities = exports.getAllLeafGroups = exports.getAllGroups = exports.getGroups = exports.getRoots = exports.MesoscaleState = exports.MesoscaleStateObject = exports.MesoscaleStateParams = exports.setGraphicsCanvas3DProps = exports.getGraphicsModeProps = exports.getLodLevels = exports.getMesoscaleGroupParams = exports.MesoscaleGroup = exports.MesoscaleGroupObject = exports.MesoscaleGroupParams = exports.createClipMapping = exports.getClipObjects = exports.SimpleClipParams = exports.LodParams = exports.PatternParams = exports.EmissiveParams = exports.OpacityParams = exports.DimLightness = exports.LightnessParams = exports.RootParams = exports.ColorValueParam = exports.ColorParams = exports.getDistinctBaseColors = exports.getDistinctGroupColors = void 0;
+exports.MesoscaleState = exports.MesoscaleStateObject = exports.MesoscaleStateParams = exports.MesoscaleGroup = exports.MesoscaleGroupObject = exports.MesoscaleGroupParams = exports.SimpleClipParams = exports.LodParams = exports.StyleParams = exports.PatternParams = exports.celShaded = exports.EmissiveParams = exports.OpacityParams = exports.IllustrativeParams = exports.DimLightness = exports.LightnessParams = exports.RootParams = exports.ColorValueParam = exports.ColorParams = void 0;
+exports.getDistinctGroupColors = getDistinctGroupColors;
+exports.getDistinctBaseColors = getDistinctBaseColors;
+exports.getClipObjects = getClipObjects;
+exports.createClipMapping = createClipMapping;
+exports.getMesoscaleGroupParams = getMesoscaleGroupParams;
+exports.getLodLevels = getLodLevels;
+exports.getGraphicsModeProps = getGraphicsModeProps;
+exports.setGraphicsCanvas3DProps = setGraphicsCanvas3DProps;
+exports.getRoots = getRoots;
+exports.getGroups = getGroups;
+exports.getAllGroups = getAllGroups;
+exports.getAllLeafGroups = getAllLeafGroups;
+exports.getEntities = getEntities;
+exports.getFilteredEntities = getFilteredEntities;
+exports.getAllEntities = getAllEntities;
+exports.getAllFilteredEntities = getAllFilteredEntities;
+exports.getEveryEntity = getEveryEntity;
+exports.getEntityLabel = getEntityLabel;
+exports.getCellDescription = getCellDescription;
+exports.getEntityDescription = getEntityDescription;
+exports.updateColors = updateColors;
+exports.expandAllGroups = expandAllGroups;
+exports.updateReprParams = updateReprParams;
 const objects_1 = require("../../../mol-plugin-state/objects");
 const param_definition_1 = require("../../../mol-util/param-definition");
 const mol_task_1 = require("../../../mol-task");
@@ -21,6 +44,7 @@ const mol_state_1 = require("../../../mol-state");
 const representation_1 = require("../../../mol-plugin-state/transforms/representation");
 const type_helpers_1 = require("../../../mol-util/type-helpers");
 const interpolate_1 = require("../../../mol-math/interpolate");
+const material_1 = require("../../../mol-util/material");
 function getHueRange(hue, variability) {
     let min = hue - variability;
     const minOverflow = (min < 0 ? -min : 0);
@@ -69,7 +93,6 @@ function getDistinctGroupColors(count, color, variability, shift, props) {
         return colors;
     }
 }
-exports.getDistinctGroupColors = getDistinctGroupColors;
 const Colors = [0x377eb8, 0xe41a1c, 0x4daf4a, 0x984ea3, 0xff7f00, 0xffff33, 0xa65628, 0xf781bf];
 function getDistinctBaseColors(count, shift, props) {
     let colors;
@@ -96,9 +119,9 @@ function getDistinctBaseColors(count, shift, props) {
         return colors;
     }
 }
-exports.getDistinctBaseColors = getDistinctBaseColors;
 exports.ColorParams = {
     type: param_definition_1.ParamDefinition.Select('generate', param_definition_1.ParamDefinition.arrayToOptions(['generate', 'uniform', 'custom'])),
+    illustrative: param_definition_1.ParamDefinition.Boolean(false, { description: 'Illustrative style', hideIf: p => p.type === 'custom' }),
     value: param_definition_1.ParamDefinition.Color((0, color_1.Color)(0xFFFFFF), { hideIf: p => p.type === 'custom' }),
     variability: param_definition_1.ParamDefinition.Numeric(20, { min: 1, max: 180, step: 1 }, { hideIf: p => p.type !== 'generate' }),
     shift: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 100, step: 1 }, { hideIf: p => !p.type.includes('generate') }),
@@ -109,6 +132,7 @@ exports.ColorParams = {
 exports.ColorValueParam = param_definition_1.ParamDefinition.Color((0, color_1.Color)(0xFFFFFF));
 exports.RootParams = {
     type: param_definition_1.ParamDefinition.Select('custom', param_definition_1.ParamDefinition.arrayToOptions(['group-generate', 'group-uniform', 'generate', 'uniform', 'custom'])),
+    illustrative: param_definition_1.ParamDefinition.Boolean(false, { description: 'Illustrative style', hideIf: p => p.type === 'custom' }),
     value: param_definition_1.ParamDefinition.Color((0, color_1.Color)(0xFFFFFF), { hideIf: p => p.type !== 'uniform' }),
     variability: param_definition_1.ParamDefinition.Numeric(20, { min: 1, max: 180, step: 1 }, { hideIf: p => p.type !== 'group-generate' }),
     shift: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 100, step: 1 }, { hideIf: p => !p.type.includes('generate') }),
@@ -120,16 +144,27 @@ exports.LightnessParams = {
     lightness: param_definition_1.ParamDefinition.Numeric(0, { min: -6, max: 6, step: 0.1 }),
 };
 exports.DimLightness = 6;
+exports.IllustrativeParams = {
+    illustrative: param_definition_1.ParamDefinition.Boolean(false, { description: 'Illustrative style' }),
+};
 exports.OpacityParams = {
     alpha: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }),
 };
 exports.EmissiveParams = {
     emissive: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 1, step: 0.01 }),
 };
+exports.celShaded = {
+    celShaded: param_definition_1.ParamDefinition.Boolean(false, { description: 'Cel Shading light for stylized rendering of representations' })
+};
 exports.PatternParams = {
     frequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }),
     amplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }),
 };
+exports.StyleParams = {
+    ignoreLight: param_definition_1.ParamDefinition.Boolean(false, { description: 'Ignore light for stylized rendering of representations' }),
+    materialStyle: material_1.Material.getParam(),
+    celShaded: param_definition_1.ParamDefinition.Boolean(false, { description: 'Cel Shading light for stylized rendering of representations' }),
+};
 exports.LodParams = {
     lodLevels: spheres_1.Spheres.Params.lodLevels,
     cellSize: spheres_1.Spheres.Params.cellSize,
@@ -168,7 +203,6 @@ function getClipObjects(values, boundingSphere) {
             rotation: values.rotation
         }];
 }
-exports.getClipObjects = getClipObjects;
 function createClipMapping(node) {
     return (0, param_mapping_1.ParamMapping)({
         params: exports.SimpleClipParams,
@@ -215,12 +249,12 @@ function createClipMapping(node) {
         }
     });
 }
-exports.createClipMapping = createClipMapping;
 exports.MesoscaleGroupParams = {
     root: param_definition_1.ParamDefinition.Value(false, { isHidden: true }),
     index: param_definition_1.ParamDefinition.Value(-1, { isHidden: true }),
     tag: param_definition_1.ParamDefinition.Value('', { isHidden: true }),
     label: param_definition_1.ParamDefinition.Value('', { isHidden: true }),
+    description: param_definition_1.ParamDefinition.Value('', { isHidden: true }),
     hidden: param_definition_1.ParamDefinition.Boolean(false),
     color: param_definition_1.ParamDefinition.Group(exports.RootParams),
     lightness: param_definition_1.ParamDefinition.Numeric(0, { min: -6, max: 6, step: 0.1 }),
@@ -241,7 +275,7 @@ exports.MesoscaleGroup = objects_1.PluginStateTransform.BuiltIn({
 })({
     apply({ a, params }, plugin) {
         return mol_task_1.Task.create('Apply Mesoscale Group', async () => {
-            return new MesoscaleGroupObject({}, { label: params.label });
+            return new MesoscaleGroupObject({}, { label: params.label, description: params.description });
         });
     },
 });
@@ -257,7 +291,6 @@ function getMesoscaleGroupParams(graphicsMode) {
         }
     };
 }
-exports.getMesoscaleGroupParams = getMesoscaleGroupParams;
 function getLodLevels(graphicsMode) {
     switch (graphicsMode) {
         case 'performance':
@@ -292,7 +325,6 @@ function getLodLevels(graphicsMode) {
             (0, type_helpers_1.assertUnreachable)(graphicsMode);
     }
 }
-exports.getLodLevels = getLodLevels;
 function getGraphicsModeProps(graphicsMode) {
     return {
         lodLevels: getLodLevels(graphicsMode),
@@ -300,7 +332,6 @@ function getGraphicsModeProps(graphicsMode) {
         alphaThickness: graphicsMode === 'performance' ? 15 : 12,
     };
 }
-exports.getGraphicsModeProps = getGraphicsModeProps;
 function setGraphicsCanvas3DProps(ctx, graphics) {
     var _a, _b;
     const pixelScale = graphics === 'balanced' ? 0.75
@@ -315,13 +346,15 @@ function setGraphicsCanvas3DProps(ctx, graphics) {
         }
     });
 }
-exports.setGraphicsCanvas3DProps = setGraphicsCanvas3DProps;
 //
 exports.MesoscaleStateParams = {
     filter: param_definition_1.ParamDefinition.Value('', { isHidden: true }),
     graphics: param_definition_1.ParamDefinition.Select('quality', param_definition_1.ParamDefinition.arrayToOptions(['ultra', 'quality', 'balanced', 'performance', 'custom'])),
     description: param_definition_1.ParamDefinition.Value('', { isHidden: true }),
+    focusInfo: param_definition_1.ParamDefinition.Value('', { isHidden: true }),
     link: param_definition_1.ParamDefinition.Value('', { isHidden: true }),
+    textSizeDescription: param_definition_1.ParamDefinition.Numeric(14, { min: 1, max: 100, step: 1 }, { isHidden: true }),
+    index: param_definition_1.ParamDefinition.Value(-1, { isHidden: true })
 };
 class MesoscaleStateObject extends objects_1.PluginStateObject.Create({ name: 'Mesoscale State', typeClass: 'Object' }) {
 }
@@ -379,7 +412,6 @@ function getRoots(plugin) {
     }
     return s.stateCache.roots;
 }
-exports.getRoots = getRoots;
 function getGroups(plugin, tag) {
     const s = plugin.customState;
     const k = `groups-${tag || ''}`;
@@ -391,7 +423,6 @@ function getGroups(plugin, tag) {
     }
     return s.stateCache[k];
 }
-exports.getGroups = getGroups;
 function _getAllGroups(plugin, tag, list) {
     var _a;
     const groups = getGroups(plugin, tag);
@@ -404,7 +435,6 @@ function _getAllGroups(plugin, tag, list) {
 function getAllGroups(plugin, tag) {
     return _getAllGroups(plugin, tag, []);
 }
-exports.getAllGroups = getAllGroups;
 function getAllLeafGroups(plugin, tag) {
     const allGroups = getAllGroups(plugin, tag);
     allGroups.sort((a, b) => { var _a, _b; return ((_a = a.params) === null || _a === void 0 ? void 0 : _a.values.index) - ((_b = b.params) === null || _b === void 0 ? void 0 : _b.values.index); });
@@ -413,7 +443,6 @@ function getAllLeafGroups(plugin, tag) {
         return getEntities(plugin, (_a = g.params) === null || _a === void 0 ? void 0 : _a.values.tag).length > 0;
     });
 }
-exports.getAllLeafGroups = getAllLeafGroups;
 function getEntities(plugin, tag) {
     const s = plugin.customState;
     const k = `entities-${tag || ''}`;
@@ -431,17 +460,17 @@ function getEntities(plugin, tag) {
     }
     return s.stateCache[k];
 }
-exports.getEntities = getEntities;
 function getFilterMatcher(filter) {
     return filter.startsWith('"') && filter.endsWith('"')
         ? new RegExp(`^${(0, string_1.escapeRegExp)(filter.substring(1, filter.length - 1))}$`, 'g')
         : new RegExp((0, string_1.escapeRegExp)(filter), 'gi');
 }
 function getFilteredEntities(plugin, tag, filter) {
+    if (!filter)
+        return getEntities(plugin, tag);
     const matcher = getFilterMatcher(filter);
     return getEntities(plugin, tag).filter(c => getEntityLabel(plugin, c).match(matcher) !== null);
 }
-exports.getFilteredEntities = getFilteredEntities;
 function _getAllEntities(plugin, tag, list) {
     var _a;
     list.push(...getEntities(plugin, tag));
@@ -453,22 +482,41 @@ function _getAllEntities(plugin, tag, list) {
 function getAllEntities(plugin, tag) {
     return _getAllEntities(plugin, tag, []);
 }
-exports.getAllEntities = getAllEntities;
 function getAllFilteredEntities(plugin, tag, filter) {
+    if (!filter)
+        return getAllEntities(plugin, tag);
     const matcher = getFilterMatcher(filter);
     return getAllEntities(plugin, tag).filter(c => getEntityLabel(plugin, c).match(matcher) !== null);
 }
-exports.getAllFilteredEntities = getAllFilteredEntities;
+function getEveryEntity(plugin, filter, tag) {
+    if (filter) {
+        const matcher = getFilterMatcher(filter);
+        return getAllEntities(plugin, tag).filter(c => getEntityLabel(plugin, c).match(matcher) !== null);
+    }
+    else {
+        return getAllEntities(plugin, tag);
+    }
+}
 function getEntityLabel(plugin, cell) {
     var _a, _b;
     return ((_b = (_a = mol_state_1.StateObjectRef.resolve(plugin.state.data, cell.transform.parent)) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.label) || 'Entity';
 }
-exports.getEntityLabel = getEntityLabel;
-//
-async function updateColors(plugin, values, tag, filter) {
+function getCellDescription(cell) {
+    var _a, _b;
+    // markdown style for description
+    return '**' + ((_a = cell === null || cell === void 0 ? void 0 : cell.obj) === null || _a === void 0 ? void 0 : _a.label) + '**\n\n' + ((_b = cell === null || cell === void 0 ? void 0 : cell.obj) === null || _b === void 0 ? void 0 : _b.description);
+}
+function getEntityDescription(plugin, cell) {
+    const s = mol_state_1.StateObjectRef.resolve(plugin.state.data, cell.transform.parent);
+    const d = getCellDescription(s);
+    return d;
+}
+async function updateColors(plugin, values, options, tag, filter) {
     var _a, _b;
     const update = plugin.state.data.build();
-    const { type, value, shift, lightness, alpha, emissive } = values;
+    const { type, illustrative, value, shift, lightness, alpha, emissive } = values;
+    const doLighting = (options !== undefined);
+    const { ignoreLight, materialStyle: material, celShaded } = options ? options : { ignoreLight: true, materialStyle: { metalness: 0, roughness: 0.2, bumpiness: 0 }, celShaded: false };
     if (type === 'group-generate' || type === 'group-uniform') {
         const groups = getAllLeafGroups(plugin, tag);
         const baseColors = getDistinctBaseColors(groups.length, shift);
@@ -484,11 +532,20 @@ async function updateColors(plugin, values, tag, filter) {
                 const c = type === 'group-generate' ? groupColors[j] : baseColors[i];
                 update.to(entities[j]).update(old => {
                     if (old.type) {
-                        old.colorTheme.params.value = c;
-                        old.colorTheme.params.lightness = lightness;
+                        if (illustrative) {
+                            old.colorTheme = { name: 'illustrative', params: { style: { name: 'uniform', params: { value: c, lightness: lightness } } } };
+                        }
+                        else {
+                            old.colorTheme = { name: 'uniform', params: { value: c, lightness: lightness } };
+                        }
                         old.type.params.alpha = alpha;
                         old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
                         old.type.params.emissive = emissive;
+                        if (doLighting) {
+                            old.type.params.ignoreLight = ignoreLight;
+                            old.type.params.material = material;
+                            old.type.params.celShaded = celShaded;
+                        }
                     }
                     else if (old.coloring) {
                         old.coloring.params.color = c;
@@ -501,6 +558,7 @@ async function updateColors(plugin, values, tag, filter) {
             }
             update.to(g.transform.ref).update(old => {
                 old.color.type = type === 'group-generate' ? 'generate' : 'uniform';
+                old.color.illustrative = illustrative;
                 old.color.value = baseColors[i];
                 old.color.lightness = lightness;
                 old.color.alpha = alpha;
@@ -518,11 +576,20 @@ async function updateColors(plugin, values, tag, filter) {
             const c = type === 'generate' ? groupColors[j] : value;
             update.to(entities[j]).update(old => {
                 if (old.type) {
-                    old.colorTheme.params.value = c;
-                    old.colorTheme.params.lightness = lightness;
+                    if (illustrative) {
+                        old.colorTheme = { name: 'illustrative', params: { style: { name: 'uniform', params: { value: c, lightness: lightness } } } };
+                    }
+                    else {
+                        old.colorTheme = { name: 'uniform', params: { value: c, lightness: lightness } };
+                    }
                     old.type.params.alpha = alpha;
                     old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
                     old.type.params.emissive = emissive;
+                    if (doLighting) {
+                        old.type.params.ignoreLight = ignoreLight;
+                        old.type.params.material = material;
+                        old.type.params.celShaded = celShaded;
+                    }
                 }
                 else if (old.coloring) {
                     old.coloring.params.color = c;
@@ -537,6 +604,7 @@ async function updateColors(plugin, values, tag, filter) {
         for (const o of others) {
             update.to(o).update(old => {
                 old.color.type = type === 'generate' ? 'custom' : 'uniform';
+                old.color.illustrative = illustrative;
                 old.color.value = value;
                 old.color.lightness = lightness;
                 old.color.alpha = alpha;
@@ -546,7 +614,6 @@ async function updateColors(plugin, values, tag, filter) {
     }
     await update.commit();
 }
-exports.updateColors = updateColors;
 ;
 function expandAllGroups(plugin) {
     for (const g of getAllGroups(plugin)) {
@@ -555,5 +622,17 @@ function expandAllGroups(plugin) {
         }
     }
 }
-exports.expandAllGroups = expandAllGroups;
 ;
+async function updateReprParams(plugin, options) {
+    const update = plugin.state.data.build();
+    const { ignoreLight, materialStyle: material, celShaded } = options;
+    const entities = getAllEntities(plugin);
+    for (let j = 0; j < entities.length; ++j) {
+        update.to(entities[j]).update(old => {
+            old.type.params.ignoreLight = ignoreLight;
+            old.type.params.material = material;
+            old.type.params.celShaded = celShaded;
+        });
+    }
+    await update.commit();
+}

package/lib/commonjs/apps/mesoscale-explorer/data/util.js

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.partitionUnits = exports.mergeUnits = void 0;
+exports.mergeUnits = mergeUnits;
+exports.partitionUnits = partitionUnits;
 const int_1 = require("../../../mol-data/int");
 const geometry_1 = require("../../../mol-math/geometry");
 const linear_algebra_1 = require("../../../mol-math/linear-algebra");
@@ -46,7 +47,6 @@ function mergeUnits(units, id) {
     }
     return structure_1.Unit.create(id, id, 0, u.traits | structure_1.Unit.Trait.MultiChain, u.kind, u.model, u.conformation.operator, elements);
 }
-exports.mergeUnits = mergeUnits;
 function partitionUnits(units, cellSize) {
     const unitCount = units.length;
     const mergedUnits = [];
@@ -78,4 +78,3 @@ function partitionUnits(units, cellSize) {
     }
     return mergedUnits;
 }
-exports.partitionUnits = partitionUnits;

package/lib/commonjs/apps/mesoscale-explorer/ui/entities.d.ts

@@ -21,6 +21,7 @@ export declare class ModelInfo extends PluginUIComponent<{}, {
     };
     componentDidMount(): void;
     get info(): {
+        selectionDescription: string;
         description: string;
         link: string;
     } | undefined;
@@ -38,6 +39,7 @@ export declare class SelectionInfo extends PluginUIComponent<{}, {
     get info(): {
         label: string;
         key: string;
+        description?: string;
     }[];
     find(label: string): void;
     remove(key: string): void;
@@ -48,6 +50,19 @@ export declare class SelectionInfo extends PluginUIComponent<{}, {
     renderStyle(): import("react/jsx-runtime").JSX.Element;
     render(): import("react/jsx-runtime").JSX.Element;
 }
+export declare function MesoMarkdownAnchor({ href, children, element }: {
+    href?: string;
+    children?: any;
+    element?: any;
+}): any;
+export declare function MesoViewportSnapshotDescription(): import("react/jsx-runtime").JSX.Element | null;
+export declare class FocusInfo extends PluginUIComponent<{}, {
+    isDisabled: boolean;
+}> {
+    componentDidMount(): void;
+    get info(): string;
+    render(): import("react/jsx-runtime").JSX.Element;
+}
 export declare class EntityControls extends PluginUIComponent<{}, {
     isDisabled: boolean;
 }> {
@@ -78,7 +93,7 @@ declare class Node<P extends {}, S extends {
     is(e: State.ObjectEvent): boolean;
     get ref(): string;
     get cell(): (P & {
-        cell: StateObjectCell<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateTransform<StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>;
+        cell: StateObjectCell;
         depth: number;
     } & {
         children?: any;
@@ -102,6 +117,7 @@ export declare class GroupNode extends Node<{
     toggleColor: (e?: React.MouseEvent<HTMLButtonElement, MouseEvent>) => void;
     toggleClip: () => void;
     toggleRoot: () => void;
+    showInfo: (e: React.MouseEvent<HTMLElement>) => void;
     highlight: (e: React.MouseEvent<HTMLElement>) => void;
     clearHighlight: (e: React.MouseEvent<HTMLElement>) => void;
     get groups(): StateSelection.CellSeq<StateObjectCell<import("../data/state").MesoscaleGroupObject, import("../../../mol-state").StateTransform<StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>>>;
@@ -162,9 +178,11 @@ export declare class EntityNode extends Node<{}, {
         index: number;
         tag: string;
         label: string;
+        description: string;
         hidden: boolean;
         color: PD.Normalize<{
             type: any;
+            illustrative: any;
             value: any;
             variability: any;
             shift: any;
@@ -198,6 +216,9 @@ export declare class EntityNode extends Node<{}, {
     center: (e: React.MouseEvent<HTMLElement>) => void;
     handleClick: (e: React.MouseEvent<HTMLElement>) => void;
     get colorValue(): Color | undefined;
+    get illustrativeValue(): {
+        illustrative: boolean;
+    } | undefined;
     get lightnessValue(): {
         lightness: number;
     } | undefined;
@@ -214,6 +235,7 @@ export declare class EntityNode extends Node<{}, {
         frequency: number;
     } | undefined;
     updateColor: ParamOnChange;
+    updateIllustrative: (values: PD.Values) => Promise<void>;
     updateLightness: (values: PD.Values) => Promise<void>;
     updateOpacity: (values: PD.Values) => Promise<void>;
     updateEmissive: (values: PD.Values) => Promise<void>;