molstar 3.0.0-dev.5 → 3.0.0-dev.9

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

@@ -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

@@ -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" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-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" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-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" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-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" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | "volume-value" | undefined;
         typeParams: {
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
             ignoreHydrogens: boolean;

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/manager/structure/component.d.ts

@@ -1,7 +1,8 @@
 /**
- * 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 David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { PluginContext } from '../../../mol-plugin/context';
 import { StateTransformer } from '../../../mol-state';
@@ -13,6 +14,7 @@ import { StatefulPluginComponent } from '../../component';
 import { StructureSelectionQuery } from '../../helpers/structure-selection-query';
 import { StructureRepresentation3D } from '../../transforms/representation';
 import { StructureHierarchyRef, StructureComponentRef, StructureRef, StructureRepresentationRef } from './hierarchy-state';
+import { Clip } from '../../../mol-util/clip';
 export { StructureComponentManager };
 interface StructureComponentManagerState {
     options: StructureComponentManager.Options;
@@ -63,6 +65,16 @@ declare namespace StructureComponentManager {
             roughness: number;
             bumpiness: number;
         }>>;
+        clipObjects: PD.Group<PD.Normalize<{
+            variant: Clip.Variant;
+            objects: PD.Normalize<{
+                type: any;
+                invert: any;
+                position: any;
+                rotation: any;
+                scale: any;
+            }>[];
+        }>>;
         interactions: PD.Group<PD.Normalize<{
             providers: PD.Normalize<{
                 ionic: any;

package/lib/mol-plugin-state/manager/structure/component.js

@@ -1,7 +1,8 @@
 /**
- * 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 David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { __assign, __awaiter, __extends, __generator, __spreadArray } from "tslib";
 import { VisualQualityOptions } from '../../../mol-geo/geometry/base';
@@ -10,7 +11,7 @@ import { Structure, StructureElement, StructureSelection } from '../../../mol-mo
 import { structureAreEqual, structureAreIntersecting, structureIntersect, structureSubtract, structureUnion } from '../../../mol-model/structure/query/utils/structure-set';
 import { setSubtreeVisibility } from '../../../mol-plugin/behavior/static/state';
 import { Task } from '../../../mol-task';
-import { UUID } from '../../../mol-util';
+import { shallowEqual, UUID } from '../../../mol-util';
 import { ColorNames } from '../../../mol-util/color/names';
 import { objectForEach } from '../../../mol-util/object';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
@@ -25,6 +26,7 @@ import { setStructureTransparency } from '../../helpers/structure-transparency';
 import { StructureFocusRepresentation } from '../../../mol-plugin/behavior/dynamic/selection/structure-focus-representation';
 import { setStructureSubstance } from '../../helpers/structure-substance';
 import { Material } from '../../../mol-util/material';
+import { Clip } from '../../../mol-util/clip';
 export { StructureComponentManager };
 var StructureComponentManager = /** @class */ (function (_super) {
     __extends(StructureComponentManager, _super);
@@ -75,6 +77,7 @@ var StructureComponentManager = /** @class */ (function (_super) {
                                     return [4 /*yield*/, this.plugin.state.updateBehavior(StructureFocusRepresentation, function (p) {
                                             p.ignoreHydrogens = !options.showHydrogens;
                                             p.material = options.materialStyle;
+                                            p.clip = options.clipObjects;
                                         })];
                                 case 2:
                                     _a.sent();
@@ -91,18 +94,19 @@ var StructureComponentManager = /** @class */ (function (_super) {
         });
     };
     StructureComponentManager.prototype.updateReprParams = function (update, component) {
-        var _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality, material = _a.materialStyle;
+        var _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality, material = _a.materialStyle, clip = _a.clipObjects;
         var ignoreHydrogens = !showHydrogens;
         for (var _i = 0, _b = component.representations; _i < _b.length; _i++) {
             var r = _b[_i];
             if (r.cell.transform.transformer !== StructureRepresentation3D)
                 continue;
             var params = r.cell.transform.params;
-            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality || params.type.params.material !== material) {
+            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality || !shallowEqual(params.type.params.material, material) || !PD.areEqual(Clip.Params, params.type.params.clip, clip)) {
                 update.to(r.cell).update(function (old) {
                     old.type.params.ignoreHydrogens = ignoreHydrogens;
                     old.type.params.quality = quality;
                     old.type.params.material = material;
+                    old.type.params.clip = clip;
                 });
             }
         }
@@ -374,9 +378,9 @@ var StructureComponentManager = /** @class */ (function (_super) {
         var _this = this;
         if (components.length === 0)
             return;
-        var _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality, material = _a.materialStyle;
+        var _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality, material = _a.materialStyle, clip = _a.clipObjects;
         var ignoreHydrogens = !showHydrogens;
-        var typeParams = { ignoreHydrogens: ignoreHydrogens, quality: quality, material: material };
+        var typeParams = { ignoreHydrogens: ignoreHydrogens, quality: quality, material: material, clip: clip };
         return this.plugin.dataTransaction(function () { return __awaiter(_this, void 0, void 0, function () {
             var _i, components_9, component;
             return __generator(this, function (_a) {
@@ -437,16 +441,16 @@ var StructureComponentManager = /** @class */ (function (_super) {
             var _this = this;
             return __generator(this, function (_a) {
                 return [2 /*return*/, this.plugin.dataTransaction(function () { return __awaiter(_this, void 0, void 0, function () {
-                        var xs, _a, showHydrogens, quality, material, ignoreHydrogens, typeParams, componentKey, _i, xs_1, s, component;
+                        var xs, _a, showHydrogens, quality, material, clip, ignoreHydrogens, typeParams, componentKey, _i, xs_1, s, component;
                         return __generator(this, function (_b) {
                             switch (_b.label) {
                                 case 0:
                                     xs = structures || this.currentStructures;
                                     if (xs.length === 0)
                                         return [2 /*return*/];
-                                    _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality, material = _a.materialStyle;
+                                    _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality, material = _a.materialStyle, clip = _a.clipObjects;
                                     ignoreHydrogens = !showHydrogens;
-                                    typeParams = { ignoreHydrogens: ignoreHydrogens, quality: quality, material: material };
+                                    typeParams = { ignoreHydrogens: ignoreHydrogens, quality: quality, material: material, clip: clip };
                                     componentKey = UUID.create22();
                                     _i = 0, xs_1 = xs;
                                     _b.label = 1;
@@ -622,6 +626,7 @@ var StructureComponentManager = /** @class */ (function (_super) {
         showHydrogens: PD.Boolean(true, { description: 'Toggle display of hydrogen atoms in representations' }),
         visualQuality: PD.Select('auto', VisualQualityOptions, { description: 'Control the visual/rendering quality of representations' }),
         materialStyle: Material.getParam(),
+        clipObjects: PD.Group(Clip.Params),
         interactions: PD.Group(InteractionsProvider.defaultParams, { label: 'Non-covalent Interactions' }),
     };
     function getAddParams(plugin, params) {

package/lib/mol-plugin-state/manager/structure/selection.js

@@ -247,7 +247,9 @@ var StructureSelectionManager = /** @class */ (function (_super) {
         var cell = this.plugin.helpers.substructureParent.get(obj.data, true);
         if (!cell)
             return;
-        ref = cell.transform.ref;
+        // only need to update the root
+        if (ref !== cell.transform.ref)
+            return;
         if (!this.entries.has(ref))
             return;
         // use structure from last decorator as reference

package/lib/mol-plugin-state/transforms/representation.d.ts

@@ -159,6 +159,10 @@ declare const ModelUnitcell3D: StateTransformer<SO.Molecule.Model, SO.Shape.Repr
         roughness: number;
         bumpiness: number;
     }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
 }>>;
 export { StructureBoundingBox3D };
 declare type StructureBoundingBox3D = typeof StructureBoundingBox3D;
@@ -177,6 +181,10 @@ declare const StructureBoundingBox3D: StateTransformer<SO.Molecule.Structure, SO
         roughness: number;
         bumpiness: number;
     }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     radius: number;
     color: Color;
 }>>;
@@ -214,6 +222,10 @@ declare const StructureSelectionsDistance3D: StateTransformer<SO.Molecule.Struct
         roughness: number;
         bumpiness: number;
     }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     lineSizeAttenuation: boolean;
     linesColor: Color;
     linesSize: number;
@@ -252,6 +264,10 @@ declare const StructureSelectionsAngle3D: StateTransformer<SO.Molecule.Structure
         roughness: number;
         bumpiness: number;
     }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     ignoreLight: boolean;
     sectorOpacity: number;
     color: Color;
@@ -299,6 +315,10 @@ declare const StructureSelectionsDihedral3D: StateTransformer<SO.Molecule.Struct
         roughness: number;
         bumpiness: number;
     }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     ignoreLight: boolean;
     sectorOpacity: number;
     color: Color;
@@ -347,6 +367,10 @@ declare const StructureSelectionsLabel3D: StateTransformer<SO.Molecule.Structure
         roughness: number;
         bumpiness: number;
     }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
 }>>;
 export { StructureSelectionsOrientation3D };
 declare type StructureSelectionsOrientation3D = typeof StructureSelectionsOrientation3D;
@@ -369,6 +393,10 @@ declare const StructureSelectionsOrientation3D: StateTransformer<SO.Molecule.Str
         roughness: number;
         bumpiness: number;
     }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
 }>>;
 export { StructureSelectionsPlane3D };
 declare type StructureSelectionsPlane3D = typeof StructureSelectionsPlane3D;
@@ -390,4 +418,8 @@ declare const StructureSelectionsPlane3D: StateTransformer<SO.Molecule.Structure
         roughness: number;
         bumpiness: number;
     }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
 }>>;

package/lib/mol-plugin-state/transforms/representation.js

@@ -85,7 +85,7 @@ var StructureRepresentation3D = PluginStateTransform.BuiltIn({
         return ({
             type: PD.Mapped(registry.default.name, registry.getApplicableTypes(a.data), function (name) { return PD.Group(registry.get(name).getParams(themeCtx, a.data)); }),
             colorTheme: PD.Mapped(type.defaultColorTheme.name, themeCtx.colorThemeRegistry.getApplicableTypes(dataCtx), function (name) { return PD.Group(themeCtx.colorThemeRegistry.get(name).getParams(dataCtx)); }, colorThemeInfo),
-            sizeTheme: PD.Mapped(type.defaultSizeTheme.name, themeCtx.sizeThemeRegistry.types, function (name) { return PD.Group(themeCtx.sizeThemeRegistry.get(name).getParams(dataCtx)); })
+            sizeTheme: PD.Mapped(type.defaultSizeTheme.name, themeCtx.sizeThemeRegistry.getApplicableTypes(dataCtx), function (name) { return PD.Group(themeCtx.sizeThemeRegistry.get(name).getParams(dataCtx)); })
         });
     }
 })({
@@ -799,7 +799,7 @@ var VolumeRepresentation3D = PluginStateTransform.BuiltIn({
         return ({
             type: PD.Mapped(registry.default.name, registry.types, function (name) { return PD.Group(registry.get(name).getParams(themeCtx, a.data)); }),
             colorTheme: PD.Mapped(type.defaultColorTheme.name, themeCtx.colorThemeRegistry.getApplicableTypes(dataCtx), function (name) { return PD.Group(themeCtx.colorThemeRegistry.get(name).getParams(dataCtx)); }),
-            sizeTheme: PD.Mapped(type.defaultSizeTheme.name, themeCtx.sizeThemeRegistry.types, function (name) { return PD.Group(themeCtx.sizeThemeRegistry.get(name).getParams(dataCtx)); })
+            sizeTheme: PD.Mapped(type.defaultSizeTheme.name, themeCtx.sizeThemeRegistry.getApplicableTypes(dataCtx), function (name) { return PD.Group(themeCtx.sizeThemeRegistry.get(name).getParams(dataCtx)); })
         });
     }
 })({

package/lib/mol-plugin-ui/index.d.ts

@@ -1,11 +1,11 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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>
  */
 import { PluginUIContext } from './context';
 import { PluginUISpec } from './spec';
-export declare function createPlugin(target: HTMLElement, spec?: PluginUISpec): PluginUIContext;
-/** Returns the instance of the plugin after all behaviors have been initialized */
-export declare function createPluginAsync(target: HTMLElement, spec?: PluginUISpec): Promise<PluginUIContext>;
+export declare function createPluginUI(target: HTMLElement, spec?: PluginUISpec, options?: {
+    onBeforeUIRender?: (ctx: PluginUIContext) => (Promise<void> | void);
+}): Promise<PluginUIContext>;