molstar 2.3.9 → 3.0.0-dev.10

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

@@ -17,6 +17,7 @@ var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 var structure_1 = require("../../../mol-model/structure");
 var util_1 = require("../../../mol-repr/util");
 var operator_name_1 = require("../../../mol-theme/color/operator-name");
+var config_1 = require("../../../mol-plugin/config");
 function TrajectoryHierarchyPresetProvider(preset) { return preset; }
 exports.TrajectoryHierarchyPresetProvider = TrajectoryHierarchyPresetProvider;
 (function (TrajectoryHierarchyPresetProvider) {
@@ -40,7 +41,7 @@ var defaultPreset = TrajectoryHierarchyPresetProvider({
     params: DefaultParams,
     apply: function (trajectory, params, plugin) {
         return (0, tslib_1.__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 (0, tslib_1.__generator)(this, function (_b) {
                 switch (_b.label) {
                     case 0:
@@ -67,7 +68,8 @@ 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(config_1.PluginConfig.Structure.DefaultRepresentationPreset) || representation_preset_1.PresetStructureRepresentations.auto.id;
+                        return [4 /*yield*/, plugin.builders.structure.representation.applyPreset(structureProperties, representationPreset, params.representationPresetParams)];
                     case 8:
                         representation = _b.sent();
                         return [2 /*return*/, {
@@ -97,7 +99,7 @@ var allModels = TrajectoryHierarchyPresetProvider({
     apply: function (trajectory, params, plugin) {
         var _a, _b;
         return (0, tslib_1.__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 (0, tslib_1.__generator)(this, function (_c) {
                 switch (_c.label) {
                     case 0:
@@ -128,7 +130,8 @@ var allModels = TrajectoryHierarchyPresetProvider({
                         models.push(model);
                         structures.push(structure);
                         quality = structure.obj ? (0, util_1.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(config_1.PluginConfig.Structure.DefaultRepresentationPreset) || representation_preset_1.PresetStructureRepresentations.auto.id;
+                        return [4 /*yield*/, builder.representation.applyPreset(structureProperties, representationPreset, { theme: { globalName: 'model-index' }, quality: quality })];
                     case 6:
                         _c.sent();
                         _c.label = 7;
@@ -144,7 +147,7 @@ var allModels = TrajectoryHierarchyPresetProvider({
 var CrystalSymmetryParams = function (a, plugin) { return ((0, tslib_1.__assign)({ model: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(mol_state_1.StateTransformer.getParamDefinition(transforms_1.StateTransforms.Model.ModelFromTrajectory, a, plugin))) }, CommonParams(a, plugin))); };
 function applyCrystalSymmetry(props, trajectory, params, plugin) {
     return (0, tslib_1.__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 (0, tslib_1.__generator)(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -167,7 +170,8 @@ 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(config_1.PluginConfig.Structure.DefaultRepresentationPreset) || representation_preset_1.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*/, {
@@ -237,7 +241,7 @@ var crystalContacts = TrajectoryHierarchyPresetProvider({
     params: CrystalContactsParams,
     apply: function (trajectory, params, plugin) {
         return (0, tslib_1.__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 (0, tslib_1.__generator)(this, function (_a) {
                 switch (_a.label) {
                     case 0:
@@ -260,7 +264,8 @@ 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: operator_name_1.OperatorNameColorThemeProvider.defaultValues } } } } })];
+                        representationPreset = params.representationPreset || plugin.config.get(config_1.PluginConfig.Structure.DefaultRepresentationPreset) || representation_preset_1.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: operator_name_1.OperatorNameColorThemeProvider.defaultValues } } } } })];
                     case 6:
                         representation = _a.sent();
                         return [2 /*return*/, {

package/lib/commonjs/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;
@@ -32,14 +32,14 @@ export declare class TrajectoryHierarchyBuilder {
             dynamicBonds: any;
         }>, "auto"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
-        }>, "model"> | PD.NamedParams<PD.Normalize<{
+            id: any;
+        }>, "assembly"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
             ijkMin: any;
             ijkMax: any;
         }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
-            id: any;
-        }>, "assembly"> | PD.NamedParams<PD.Normalize<{
+        }>, "model"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
             radius: any;
         }>, "symmetry-mates"> | PD.NamedParams<PD.Normalize<{
@@ -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/commonjs/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>
@@ -29,11 +29,11 @@ export declare namespace StructureRepresentationPresetProvider {
     };
     const CommonParams: {
         ignoreHydrogens: PD.Base<boolean | undefined>;
-        quality: PD.Base<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined>;
+        quality: PD.Base<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined>;
         theme: PD.Base<PD.Normalize<{
-            globalName: "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
-            carbonColor: "chain-id" | "operator-name" | "element-symbol" | undefined;
-            symmetryColor: "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | 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" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
             focus: PD.Normalize<{
                 name: any;
                 params: any;
@@ -44,37 +44,37 @@ 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" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
-        symmetryColor: "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | 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: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+            quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
             ignoreHydrogens: boolean;
         };
         ballAndStickColor: Partial<PD.Values<{
-            carbonColor: PD.Mapped<PD.NamedParams<PD.Normalize<{
+            carbonColor: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "element-symbol"> | PD.NamedParams<PD.Normalize<{
                 palette: PD.NamedParams<PD.Normalize<{
-                    list: any;
-                }>, "colors"> | PD.NamedParams<PD.Normalize<{
                     maxCount: any;
                     hue: any;
                     chroma: any;
                     luminance: any;
                     clusteringStepCount: any;
                     minSampleCount: any;
-                }>, "generate">;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
                 asymId: "label" | "auth";
             }>, "chain-id"> | PD.NamedParams<PD.Normalize<{
                 palette: PD.NamedParams<PD.Normalize<{
-                    list: any;
-                }>, "colors"> | PD.NamedParams<PD.Normalize<{
                     maxCount: any;
                     hue: any;
                     chroma: any;
                     luminance: any;
                     clusteringStepCount: any;
                     minSampleCount: any;
-                }>, "generate">;
-            }>, "operator-name"> | PD.NamedParams<PD.Normalize<unknown>, "element-symbol">>;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
+            }>, "operator-name">>;
             saturation: PD.Numeric;
             lightness: PD.Numeric;
         }>>;
@@ -94,7 +94,7 @@ export declare const PresetStructureRepresentations: {
     empty: StructureRepresentationPresetProvider<unknown, {}>;
     auto: StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -123,7 +123,7 @@ export declare const PresetStructureRepresentations: {
     'atomic-detail': StructureRepresentationPresetProvider<{
         showCarbohydrateSymbol: boolean;
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -144,7 +144,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'polymer-cartoon': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -164,7 +164,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'polymer-and-ligand': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -199,7 +199,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'protein-and-nucleic': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -221,7 +221,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'coarse-surface': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -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/commonjs/mol-plugin-state/builder/structure/representation-preset.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -21,6 +21,8 @@ var operator_name_1 = require("../../../mol-theme/color/operator-name");
 var index_pair_1 = require("../../../mol-model-formats/structure/property/bonds/index-pair");
 var struct_conn_1 = require("../../../mol-model-formats/structure/property/bonds/struct_conn");
 var type_helpers_1 = require("../../../mol-util/type-helpers");
+var color_1 = require("../../../mol-util/color");
+var postprocessing_1 = require("../../../mol-canvas3d/passes/postprocessing");
 function StructureRepresentationPresetProvider(repr) { return repr; }
 exports.StructureRepresentationPresetProvider = StructureRepresentationPresetProvider;
 (function (StructureRepresentationPresetProvider) {
@@ -81,6 +83,14 @@ exports.StructureRepresentationPresetProvider = StructureRepresentationPresetPro
 var CommonParams = StructureRepresentationPresetProvider.CommonParams;
 var reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
 var updateFocusRepr = StructureRepresentationPresetProvider.updateFocusRepr;
+function resetPostprocessingProps(plugin) {
+    if (plugin.canvas3d) {
+        var p = param_definition_1.ParamDefinition.getDefaultValues(postprocessing_1.PostprocessingParams);
+        plugin.canvas3d.setProps({
+            postprocessing: { outline: p.outline, occlusion: p.occlusion }
+        });
+    }
+}
 var auto = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-auto',
     display: {
@@ -120,6 +130,7 @@ var empty = StructureRepresentationPresetProvider({
     apply: function (ref, params, plugin) {
         return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
             return (0, tslib_1.__generator)(this, function (_a) {
+                resetPostprocessingProps(plugin);
                 return [2 /*return*/, {}];
             });
         });
@@ -194,6 +205,7 @@ 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 }];
                 }
             });
@@ -245,6 +257,7 @@ 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 }];
                 }
             });
@@ -311,6 +324,7 @@ 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 }];
                 }
             });
@@ -354,6 +368,7 @@ 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 }];
                 }
             });
@@ -431,6 +446,62 @@ 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 ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, CommonParams), { showCarbohydrateSymbol: param_definition_1.ParamDefinition.Boolean(false) })); },
+    apply: function (ref, params, plugin) {
+        var _a, _b, _c, _d, _e;
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var structureCell, components, structure, _f, update, builder, typeParams, color, representations;
+            var _g;
+            return (0, tslib_1.__generator)(this, function (_h) {
+                switch (_h.label) {
+                    case 0:
+                        structureCell = mol_state_1.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: (0, tslib_1.__assign)((0, tslib_1.__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: (0, color_1.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 }];
                 }
             });
@@ -452,6 +523,7 @@ exports.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/commonjs/mol-plugin-state/builder/structure/representation.d.ts

@@ -17,7 +17,7 @@ export declare class StructureRepresentationBuilder {
     private get dataState();
     readonly defaultProvider: StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;

package/lib/commonjs/mol-plugin-state/formats/volume.d.ts

@@ -71,14 +71,14 @@ export declare const CubeProvider: {
                 dynamicBonds: any;
             }>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
-            }>, "model"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+                id: any;
+            }>, "assembly"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
                 ijkMin: any;
                 ijkMax: any;
             }>, "symmetry"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
-                id: any;
-            }>, "assembly"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+            }>, "model"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
                 radius: any;
             }>, "symmetry-mates"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
@@ -152,14 +152,14 @@ export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
                 dynamicBonds: any;
             }>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
-            }>, "model"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+                id: any;
+            }>, "assembly"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
                 ijkMin: any;
                 ijkMax: any;
             }>, "symmetry"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
-                id: any;
-            }>, "assembly"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+            }>, "model"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
                 radius: any;
             }>, "symmetry-mates"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{

package/lib/commonjs/mol-plugin-state/formats/volume.js

@@ -43,6 +43,7 @@ function tryObtainRecommendedIsoValue(plugin, volume) {
                                 return [3 /*break*/, 3];
                             case 2:
                                 e_1 = _a.sent();
+                                console.warn(e_1);
                                 return [3 /*break*/, 3];
                             case 3: return [2 /*return*/];
                         }

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

@@ -16,14 +16,14 @@ export declare namespace RootStructureDefinition {
             dynamicBonds: boolean | undefined;
         }>, "auto"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
-        }>, "model"> | PD.NamedParams<PD.Normalize<{
+            id: string | undefined;
+        }>, "assembly"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
             ijkMin: Vec3;
             ijkMax: Vec3;
         }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
-            id: string | undefined;
-        }>, "assembly"> | PD.NamedParams<PD.Normalize<{
+        }>, "model"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
             radius: number;
         }>, "symmetry-mates"> | PD.NamedParams<PD.Normalize<{

package/lib/commonjs/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>