molstar 3.0.0-dev.0 → 3.0.0-dev.10

package/lib/mol-plugin-state/builder/structure/hierarchy-preset.js

@@ -9,11 +9,12 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { StateObjectRef, StateTransformer } from '../../../mol-state';
 import { StateTransforms } from '../../transforms';
 import { RootStructureDefinition } from '../../helpers/root-structure';
-import { StructureRepresentationPresetProvider } from './representation-preset';
+import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from './representation-preset';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { Model } from '../../../mol-model/structure';
 import { getStructureQuality } from '../../../mol-repr/util';
 import { OperatorNameColorThemeProvider } from '../../../mol-theme/color/operator-name';
+import { PluginConfig } from '../../../mol-plugin/config';
 export function TrajectoryHierarchyPresetProvider(preset) { return preset; }
 (function (TrajectoryHierarchyPresetProvider) {
     TrajectoryHierarchyPresetProvider.CommonParams = function (a, plugin) { return ({
@@ -36,7 +37,7 @@ var defaultPreset = TrajectoryHierarchyPresetProvider({
     params: DefaultParams,
     apply: function (trajectory, params, plugin) {
         return __awaiter(this, void 0, void 0, function () {
-            var builder, model, modelProperties, structure, structureProperties, unitcell, _a, representation;
+            var builder, model, modelProperties, structure, structureProperties, unitcell, _a, representationPreset, representation;
             return __generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
@@ -63,7 +64,8 @@ var defaultPreset = TrajectoryHierarchyPresetProvider({
                         _b.label = 7;
                     case 7:
                         unitcell = _a;
-                        return [4 /*yield*/, plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', params.representationPresetParams)];
+                        representationPreset = params.representationPreset || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+                        return [4 /*yield*/, plugin.builders.structure.representation.applyPreset(structureProperties, representationPreset, params.representationPresetParams)];
                     case 8:
                         representation = _b.sent();
                         return [2 /*return*/, {
@@ -93,7 +95,7 @@ var allModels = TrajectoryHierarchyPresetProvider({
     apply: function (trajectory, params, plugin) {
         var _a, _b;
         return __awaiter(this, void 0, void 0, function () {
-            var tr, builder, models, structures, i, model, modelProperties, structure, structureProperties, quality;
+            var tr, builder, models, structures, i, model, modelProperties, structure, structureProperties, quality, representationPreset;
             return __generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
@@ -124,7 +126,8 @@ var allModels = TrajectoryHierarchyPresetProvider({
                         models.push(model);
                         structures.push(structure);
                         quality = structure.obj ? getStructureQuality(structure.obj.data, { elementCountFactor: tr.frameCount }) : 'medium';
-                        return [4 /*yield*/, builder.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: 'model-index' }, quality: quality })];
+                        representationPreset = params.representationPreset || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+                        return [4 /*yield*/, builder.representation.applyPreset(structureProperties, representationPreset, { theme: { globalName: 'model-index' }, quality: quality })];
                     case 6:
                         _c.sent();
                         _c.label = 7;
@@ -140,7 +143,7 @@ var allModels = TrajectoryHierarchyPresetProvider({
 var CrystalSymmetryParams = function (a, plugin) { return (__assign({ model: PD.Optional(PD.Group(StateTransformer.getParamDefinition(StateTransforms.Model.ModelFromTrajectory, a, plugin))) }, CommonParams(a, plugin))); };
 function applyCrystalSymmetry(props, trajectory, params, plugin) {
     return __awaiter(this, void 0, void 0, function () {
-        var builder, model, modelProperties, structure, structureProperties, unitcell, representation;
+        var builder, model, modelProperties, structure, structureProperties, unitcell, representationPreset, representation;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -163,7 +166,8 @@ function applyCrystalSymmetry(props, trajectory, params, plugin) {
                     return [4 /*yield*/, builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: false })];
                 case 5:
                     unitcell = _a.sent();
-                    return [4 /*yield*/, plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: props.theme } })];
+                    representationPreset = params.representationPreset || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+                    return [4 /*yield*/, plugin.builders.structure.representation.applyPreset(structureProperties, representationPreset, { theme: { globalName: props.theme } })];
                 case 6:
                     representation = _a.sent();
                     return [2 /*return*/, {
@@ -233,7 +237,7 @@ var crystalContacts = TrajectoryHierarchyPresetProvider({
     params: CrystalContactsParams,
     apply: function (trajectory, params, plugin) {
         return __awaiter(this, void 0, void 0, function () {
-            var builder, model, modelProperties, structure, structureProperties, unitcell, representation;
+            var builder, model, modelProperties, structure, structureProperties, unitcell, representationPreset, representation;
             return __generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
@@ -256,7 +260,8 @@ var crystalContacts = TrajectoryHierarchyPresetProvider({
                         return [4 /*yield*/, builder.tryCreateUnitcell(modelProperties, undefined, { isHidden: true })];
                     case 5:
                         unitcell = _a.sent();
-                        return [4 /*yield*/, plugin.builders.structure.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: 'operator-name', carbonColor: 'operator-name', focus: { name: 'element-symbol', params: { carbonColor: { name: 'operator-name', params: OperatorNameColorThemeProvider.defaultValues } } } } })];
+                        representationPreset = params.representationPreset || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+                        return [4 /*yield*/, plugin.builders.structure.representation.applyPreset(structureProperties, representationPreset, { theme: { globalName: 'operator-name', carbonColor: 'operator-name', focus: { name: 'element-symbol', params: { carbonColor: { name: 'operator-name', params: OperatorNameColorThemeProvider.defaultValues } } } } })];
                     case 6:
                         representation = _a.sent();
                         return [2 /*return*/, {

package/lib/mol-plugin-state/builder/structure/hierarchy.d.ts

@@ -23,7 +23,7 @@ export declare class TrajectoryHierarchyBuilder {
             autoAttach: any;
             properties: any;
         }>> | undefined;
-        representationPreset: "auto" | "empty" | "atomic-detail" | "polymer-cartoon" | "polymer-and-ligand" | "protein-and-nucleic" | "coarse-surface" | undefined;
+        representationPreset: "auto" | "empty" | "illustrative" | "atomic-detail" | "polymer-cartoon" | "polymer-and-ligand" | "protein-and-nucleic" | "coarse-surface" | undefined;
         model: PD.Normalize<PD.Normalize<{
             modelIndex: any;
         }>> | undefined;
@@ -57,77 +57,7 @@ export declare class TrajectoryHierarchyBuilder {
         unitcell: import("../../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
         structure: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
         structureProperties: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-        representation: {} | {
-            components?: undefined;
-            representations?: undefined;
-        } | {
-            components: {
-                polymer: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-                lipid: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-            };
-            representations: {
-                polymer: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-                lipid: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-            };
-        } | {
-            components?: undefined;
-            representations?: undefined;
-        } | {
-            components: {
-                polymer: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-            };
-            representations: {
-                polymer: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-            };
-        } | {
-            components?: undefined;
-            representations?: undefined;
-        } | {
-            components: {
-                polymer: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-                ligand: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-                nonStandard: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-                branched: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-                water: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-                ion: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-                lipid: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-                coarse: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-            };
-            representations: {
-                polymer: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-                ligand: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-                nonStandard: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-                branchedBallAndStick: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-                branchedSnfg3d: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-                water: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-                ion: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-                lipid: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-                coarse: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-            };
-        } | {
-            components?: undefined;
-            representations?: undefined;
-        } | {
-            components: {
-                all: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-                branched: undefined;
-            };
-            representations: {
-                all: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-            };
-        } | {
-            components?: undefined;
-            representations?: undefined;
-        } | {
-            components: {
-                protein: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-                nucleic: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-            };
-            representations: {
-                protein: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-                nucleic: import("../../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
-            };
-        } | undefined;
+        representation: any;
     }>;
     private resolveProvider;
     hasPreset(t: PluginStateObject.Molecule.Trajectory): boolean;

package/lib/mol-plugin-state/builder/structure/representation-preset.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -31,9 +31,9 @@ export declare namespace StructureRepresentationPresetProvider {
         ignoreHydrogens: PD.Base<boolean | undefined>;
         quality: PD.Base<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined>;
         theme: PD.Base<PD.Normalize<{
-            globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
+            globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
             carbonColor: "element-symbol" | "chain-id" | "operator-name" | undefined;
-            symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
+            symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
             focus: PD.Normalize<{
                 name: any;
                 params: any;
@@ -44,8 +44,8 @@ export declare namespace StructureRepresentationPresetProvider {
     function reprBuilder(plugin: PluginContext, params: CommonParams, structure?: Structure): {
         update: import("../../../mol-state/state/builder").StateBuilder.Root;
         builder: import("./representation").StructureRepresentationBuilder;
-        color: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
-        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
+        color: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
+        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
         typeParams: {
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
             ignoreHydrogens: boolean;
@@ -241,6 +241,28 @@ export declare const PresetStructureRepresentations: {
             lipid: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
         };
     }>;
+    illustrative: StructureRepresentationPresetProvider<{
+        showCarbohydrateSymbol: boolean;
+        ignoreHydrogens: boolean | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+        theme: PD.Normalize<{
+            globalName: any;
+            carbonColor: any;
+            symmetryColor: any;
+            focus: any;
+        }> | undefined;
+    }, {
+        components?: undefined;
+        representations?: undefined;
+    } | {
+        components: {
+            all: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+            branched: undefined;
+        };
+        representations: {
+            all: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+        };
+    }>;
 };
 export declare type PresetStructureRepresentations = typeof PresetStructureRepresentations;
 export {};

package/lib/mol-plugin-state/builder/structure/representation-preset.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -18,6 +18,8 @@ import { OperatorNameColorThemeProvider } from '../../../mol-theme/color/operato
 import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bonds/index-pair';
 import { StructConn } from '../../../mol-model-formats/structure/property/bonds/struct_conn';
 import { assertUnreachable } from '../../../mol-util/type-helpers';
+import { Color } from '../../../mol-util/color';
+import { PostprocessingParams } from '../../../mol-canvas3d/passes/postprocessing';
 export function StructureRepresentationPresetProvider(repr) { return repr; }
 (function (StructureRepresentationPresetProvider) {
     StructureRepresentationPresetProvider.CommonParams = {
@@ -77,6 +79,14 @@ export function StructureRepresentationPresetProvider(repr) { return repr; }
 var CommonParams = StructureRepresentationPresetProvider.CommonParams;
 var reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
 var updateFocusRepr = StructureRepresentationPresetProvider.updateFocusRepr;
+function resetPostprocessingProps(plugin) {
+    if (plugin.canvas3d) {
+        var p = PD.getDefaultValues(PostprocessingParams);
+        plugin.canvas3d.setProps({
+            postprocessing: { outline: p.outline, occlusion: p.occlusion }
+        });
+    }
+}
 var auto = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-auto',
     display: {
@@ -116,6 +126,7 @@ var empty = StructureRepresentationPresetProvider({
     apply: function (ref, params, plugin) {
         return __awaiter(this, void 0, void 0, function () {
             return __generator(this, function (_a) {
+                resetPostprocessingProps(plugin);
                 return [2 /*return*/, {}];
             });
         });
@@ -190,6 +201,7 @@ var polymerAndLigand = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_h = (_g = params.theme) === null || _g === void 0 ? void 0 : _g.focus) === null || _h === void 0 ? void 0 : _h.name, (_k = (_j = params.theme) === null || _j === void 0 ? void 0 : _j.focus) === null || _k === void 0 ? void 0 : _k.params)];
                     case 10:
                         _o.sent();
+                        resetPostprocessingProps(plugin);
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -241,6 +253,7 @@ var proteinAndNucleic = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_b = (_a = params.theme) === null || _a === void 0 ? void 0 : _a.focus) === null || _b === void 0 ? void 0 : _b.name, (_d = (_c = params.theme) === null || _c === void 0 ? void 0 : _c.focus) === null || _d === void 0 ? void 0 : _d.params)];
                     case 4:
                         _g.sent();
+                        resetPostprocessingProps(plugin);
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -307,6 +320,7 @@ var coarseSurface = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_b = (_a = params.theme) === null || _a === void 0 ? void 0 : _a.focus) === null || _b === void 0 ? void 0 : _b.name, (_d = (_c = params.theme) === null || _c === void 0 ? void 0 : _c.focus) === null || _d === void 0 ? void 0 : _d.params)];
                     case 4:
                         _g.sent();
+                        resetPostprocessingProps(plugin);
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -350,6 +364,7 @@ var polymerCartoon = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_b = (_a = params.theme) === null || _a === void 0 ? void 0 : _a.focus) === null || _b === void 0 ? void 0 : _b.name, (_d = (_c = params.theme) === null || _c === void 0 ? void 0 : _c.focus) === null || _d === void 0 ? void 0 : _d.params)];
                     case 3:
                         _g.sent();
+                        resetPostprocessingProps(plugin);
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -427,6 +442,62 @@ var atomicDetail = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_c = (_b = (_a = params.theme) === null || _a === void 0 ? void 0 : _a.focus) === null || _b === void 0 ? void 0 : _b.name) !== null && _c !== void 0 ? _c : color, (_f = (_e = (_d = params.theme) === null || _d === void 0 ? void 0 : _d.focus) === null || _e === void 0 ? void 0 : _e.params) !== null && _f !== void 0 ? _f : colorParams)];
                     case 5:
                         _o.sent();
+                        resetPostprocessingProps(plugin);
+                        return [2 /*return*/, { components: components, representations: representations }];
+                }
+            });
+        });
+    }
+});
+var illustrative = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-illustrative',
+    display: {
+        name: 'Illustrative', group: 'Miscellaneous',
+        description: '...'
+    },
+    params: function () { return (__assign(__assign({}, CommonParams), { showCarbohydrateSymbol: PD.Boolean(false) })); },
+    apply: function (ref, params, plugin) {
+        var _a, _b, _c, _d, _e;
+        return __awaiter(this, void 0, void 0, function () {
+            var structureCell, components, structure, _f, update, builder, typeParams, color, representations;
+            var _g;
+            return __generator(this, function (_h) {
+                switch (_h.label) {
+                    case 0:
+                        structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+                        if (!structureCell)
+                            return [2 /*return*/, {}];
+                        _g = {};
+                        return [4 /*yield*/, presetStaticComponent(plugin, structureCell, 'all')];
+                    case 1:
+                        components = (_g.all = _h.sent(),
+                            _g.branched = undefined,
+                            _g);
+                        structure = structureCell.obj.data;
+                        _f = reprBuilder(plugin, params, structure), update = _f.update, builder = _f.builder, typeParams = _f.typeParams, color = _f.color;
+                        representations = {
+                            all: builder.buildRepresentation(update, components.all, { type: 'spacefill', typeParams: __assign(__assign({}, typeParams), { ignoreLight: true }), color: 'illustrative' }, { tag: 'all' }),
+                        };
+                        return [4 /*yield*/, update.commit({ revertOnError: true })];
+                    case 2:
+                        _h.sent();
+                        return [4 /*yield*/, updateFocusRepr(plugin, structure, (_c = (_b = (_a = params.theme) === null || _a === void 0 ? void 0 : _a.focus) === null || _b === void 0 ? void 0 : _b.name) !== null && _c !== void 0 ? _c : color, (_e = (_d = params.theme) === null || _d === void 0 ? void 0 : _d.focus) === null || _e === void 0 ? void 0 : _e.params)];
+                    case 3:
+                        _h.sent();
+                        if (plugin.canvas3d) {
+                            plugin.canvas3d.setProps({
+                                postprocessing: {
+                                    outline: {
+                                        name: 'on',
+                                        params: { scale: 1, color: Color(0x000000), threshold: 0.25 }
+                                    },
+                                    occlusion: {
+                                        name: 'on',
+                                        params: { bias: 0.9, blurKernelSize: 15, radius: 5, samples: 32 }
+                                    },
+                                }
+                            });
+                        }
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -446,6 +517,7 @@ export var PresetStructureRepresentations = {
     'polymer-cartoon': polymerCartoon,
     'polymer-and-ligand': polymerAndLigand,
     'protein-and-nucleic': proteinAndNucleic,
-    'coarse-surface': coarseSurface
+    'coarse-surface': coarseSurface,
+    'illustrative': illustrative,
 };
 //# sourceMappingURL=representation-preset.js.map

package/lib/mol-plugin-state/helpers/structure-clipping.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>

package/lib/mol-plugin-state/helpers/structure-clipping.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>

package/lib/mol-plugin-state/helpers/structure-selection-query.js

@@ -6,7 +6,7 @@
  */
 import { __awaiter, __generator, __spreadArray } from "tslib";
 import { QueryContext, StructureSelection, StructureProperties, StructureElement } from '../../mol-model/structure';
-import { NucleicBackboneAtoms, ProteinBackboneAtoms, AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames } from '../../mol-model/structure/model/types';
+import { NucleicBackboneAtoms, ProteinBackboneAtoms, AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames, PolymerNames } from '../../mol-model/structure/model/types';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { compile } from '../../mol-script/runtime/query/compiler';
 import { SetUtils } from '../../mol-util/set';
@@ -285,33 +285,47 @@ var branchedConnectedOnly = StructureSelectionQuery('Connected to Carbohydrate',
     })
 ]), { category: StructureSelectionCategory.Internal, isHidden: true });
 var ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
-    MS.struct.combinator.merge([
-        MS.struct.modifier.union([
-            MS.struct.generator.atomGroups({
-                'entity-test': MS.core.logic.and([
-                    MS.core.logic.or([
-                        MS.core.rel.eq([MS.ammp('entityType'), 'non-polymer']),
-                        MS.core.rel.neq([MS.ammp('entityPrdId'), ''])
-                    ]),
-                    MS.core.logic.not([MS.core.str.match([
-                            MS.re('(oligosaccharide|lipid|ion)', 'i'),
-                            MS.ammp('entitySubtype')
-                        ])])
+    MS.struct.modifier.exceptBy({
+        0: MS.struct.modifier.union([
+            MS.struct.combinator.merge([
+                MS.struct.modifier.union([
+                    MS.struct.generator.atomGroups({
+                        'entity-test': MS.core.logic.and([
+                            MS.core.logic.or([
+                                MS.core.rel.eq([MS.ammp('entityType'), 'non-polymer']),
+                                MS.core.rel.neq([MS.ammp('entityPrdId'), ''])
+                            ]),
+                            MS.core.logic.not([MS.core.str.match([
+                                    MS.re('(oligosaccharide|lipid|ion)', 'i'),
+                                    MS.ammp('entitySubtype')
+                                ])])
+                        ]),
+                        'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                        'residue-test': MS.core.logic.not([
+                            MS.core.str.match([MS.re('saccharide', 'i'), MS.ammp('chemCompType')])
+                        ])
+                    })
                 ]),
-                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
-                'residue-test': MS.core.logic.not([
-                    MS.core.str.match([MS.re('saccharide', 'i'), MS.ammp('chemCompType')])
+                MS.struct.modifier.union([
+                    MS.struct.generator.atomGroups({
+                        'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
+                        'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                        'residue-test': _nonPolymerResidueTest
+                    })
                 ])
-            })
+            ]),
         ]),
-        MS.struct.modifier.union([
+        by: MS.struct.modifier.union([
             MS.struct.generator.atomGroups({
                 'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
                 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
-                'residue-test': _nonPolymerResidueTest
+                'residue-test': MS.core.set.has([
+                    MS.set.apply(MS, SetUtils.toArray(PolymerNames)),
+                    MS.ammp('label_comp_id')
+                ])
             })
         ])
-    ]),
+    })
 ]), { category: StructureSelectionCategory.Type });
 // don't include branched entities as they have their own link representation
 var ligandPlusConnected = StructureSelectionQuery('Ligand with Connected', MS.struct.modifier.union([

package/lib/mol-plugin-state/helpers/structure-substance.d.ts

@@ -9,5 +9,5 @@ import { PluginContext } from '../../mol-plugin/context';
 import { StructureComponentRef } from '../manager/structure/hierarchy-state';
 import { EmptyLoci } from '../../mol-model/loci';
 import { Material } from '../../mol-util/material';
-export declare function setStructureSubstance(plugin: PluginContext, components: StructureComponentRef[], material: Material | -1, lociGetter: (structure: Structure) => Promise<StructureElement.Loci | EmptyLoci>, types?: string[]): Promise<void>;
+export declare function setStructureSubstance(plugin: PluginContext, components: StructureComponentRef[], material: Material | undefined, lociGetter: (structure: Structure) => Promise<StructureElement.Loci | EmptyLoci>, types?: string[]): Promise<void>;
 export declare function clearStructureSubstance(plugin: PluginContext, components: StructureComponentRef[], types?: string[]): Promise<void>;

package/lib/mol-plugin-state/helpers/structure-substance.js

@@ -32,8 +32,8 @@ export function setStructureSubstance(plugin, components, material, lociGetter,
                                         return [2 /*return*/];
                                     layer = {
                                         bundle: StructureElement.Bundle.fromLoci(loci),
-                                        material: material === -1 ? Material(0) : material,
-                                        clear: material === -1
+                                        material: material !== null && material !== void 0 ? material : Material(),
+                                        clear: !material
                                     };
                                     if (substanceCell) {
                                         bundleLayers = __spreadArray(__spreadArray([], substanceCell.params.values.layers, true), [layer], false);

package/lib/mol-plugin-state/manager/animation.d.ts

@@ -29,7 +29,7 @@ declare class PluginAnimationManager extends StatefulPluginComponent<PluginAnima
     updateCurrentParams(values: any): void;
     register(animation: PluginStateAnimation): void;
     play<P>(animation: PluginStateAnimation<P>, params: P): Promise<void>;
-    tick(t: number, isSynchronous?: boolean): Promise<void>;
+    tick(t: number, isSynchronous?: boolean, animation?: PluginAnimationManager.AnimationInfo): Promise<void>;
     private isStopped;
     private isApplying;
     start(): Promise<void>;
@@ -43,6 +43,10 @@ declare class PluginAnimationManager extends StatefulPluginComponent<PluginAnima
     constructor(context: PluginContext);
 }
 declare namespace PluginAnimationManager {
+    interface AnimationInfo {
+        currentFrame: number;
+        frameCount: number;
+    }
     interface Current {
         anim: PluginStateAnimation;
         params: PD.Params;

package/lib/mol-plugin-state/manager/animation.js

@@ -113,7 +113,7 @@ var PluginAnimationManager = /** @class */ (function (_super) {
             });
         });
     };
-    PluginAnimationManager.prototype.tick = function (t, isSynchronous) {
+    PluginAnimationManager.prototype.tick = function (t, isSynchronous, animation) {
         return __awaiter(this, void 0, void 0, function () {
             return __generator(this, function (_a) {
                 switch (_a.label) {
@@ -121,8 +121,8 @@ var PluginAnimationManager = /** @class */ (function (_super) {
                         this.currentTime = t;
                         if (this.isStopped)
                             return [2 /*return*/];
-                        if (!isSynchronous) return [3 /*break*/, 2];
-                        return [4 /*yield*/, this.applyFrame()];
+                        if (!(isSynchronous || animation)) return [3 /*break*/, 2];
+                        return [4 /*yield*/, this.applyFrame(animation)];
                     case 1:
                         _a.sent();
                         return [3 /*break*/, 3];
@@ -221,7 +221,7 @@ var PluginAnimationManager = /** @class */ (function (_super) {
             });
         });
     };
-    PluginAnimationManager.prototype.applyFrame = function () {
+    PluginAnimationManager.prototype.applyFrame = function (animation) {
         return __awaiter(this, void 0, void 0, function () {
             var t, newState;
             return __generator(this, function (_a) {
@@ -230,7 +230,7 @@ var PluginAnimationManager = /** @class */ (function (_super) {
                         t = this.currentTime;
                         if (this._current.startedTime < 0)
                             this._current.startedTime = t;
-                        return [4 /*yield*/, this._current.anim.apply(this._current.state, { lastApplied: this._current.lastTime, current: t - this._current.startedTime }, { params: this._current.paramValues, plugin: this.context })];
+                        return [4 /*yield*/, this._current.anim.apply(this._current.state, { lastApplied: this._current.lastTime, current: t - this._current.startedTime, animation: animation }, { params: this._current.paramValues, plugin: this.context })];
                     case 1:
                         newState = _a.sent();
                         if (newState.kind === 'finished') {