molstar 4.3.0 → 4.4.0

package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 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>

package/lib/commonjs/mol-plugin/util/viewport-screenshot.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 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>
@@ -86,6 +86,7 @@ class ViewportScreenshotHelper extends component_1.PluginComponent {
                 ...c.props.multiSample,
                 mode: multisample ? 'on' : 'off',
                 sampleLevel: colorBufferFloat && textureFloat ? 4 : 2,
+                reuseOcclusion: false,
             },
             postprocessing: {
                 ...c.props.postprocessing,

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 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>

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 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>
@@ -25,7 +25,7 @@ const DownloadDensity = mol_state_1.StateAction.build({
                 'pdb-xray': param_definition_1.ParamDefinition.Group({
                     provider: param_definition_1.ParamDefinition.Group({
                         id: param_definition_1.ParamDefinition.Text('1tqn', { label: 'Id' }),
-                        server: param_definition_1.ParamDefinition.Select('rcsb', [['pdbe', 'PDBe'], ['rcsb', 'RCSB PDB']]),
+                        server: param_definition_1.ParamDefinition.Select('pdbe', [['pdbe', 'PDBe']]),
                     }, { pivot: 'id' }),
                     type: param_definition_1.ParamDefinition.Select('2fofc', [['2fofc', '2Fo-Fc'], ['fofc', 'Fo-Fc']]),
                 }, { isFlat: true }),
@@ -68,18 +68,12 @@ const DownloadDensity = mol_state_1.StateAction.build({
             downloadParams = src.params;
             break;
         case 'pdb-xray':
-            downloadParams = src.params.provider.server === 'pdbe' ? {
+            downloadParams = {
                 url: assets_1.Asset.Url(src.params.type === '2fofc'
                     ? `https://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}.ccp4`
                     : `https://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}_diff.ccp4`),
                 isBinary: true,
                 label: `PDBe X-ray map: ${src.params.provider.id}`
-            } : {
-                url: assets_1.Asset.Url(src.params.type === '2fofc'
-                    ? `https://edmaps.rcsb.org/maps/${src.params.provider.id.toLowerCase()}_2fofc.dsn6`
-                    : `https://edmaps.rcsb.org/maps/${src.params.provider.id.toLowerCase()}_fofc.dsn6`),
-                isBinary: true,
-                label: `RCSB X-ray map: ${src.params.provider.id}`
             };
             break;
         case 'pdb-emd-ds':
@@ -115,9 +109,7 @@ const DownloadDensity = mol_state_1.StateAction.build({
             break;
         case 'pdb-xray':
             entryId = src.params.provider.id;
-            provider = src.params.provider.server === 'pdbe'
-                ? plugin.dataFormats.get('ccp4')
-                : plugin.dataFormats.get('dsn6');
+            provider = plugin.dataFormats.get('ccp4');
             break;
         case 'pdb-emd-ds':
         case 'pdb-xray-ds':

package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.d.ts

@@ -20,6 +20,6 @@ export declare const AnimateModelIndex: PluginStateAnimation<{
     }>, "computed">;
 }, {
     palindromeDirections?: {
-        [id: string]: 1 | -1 | undefined;
-    } | undefined;
+        [id: string]: -1 | 1 | undefined;
+    };
 }>;

package/lib/commonjs/mol-plugin-state/animation/helpers.js

@@ -6,7 +6,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.spinStructure = exports.getSpinStructureAxisAndOrigin = exports.SpinStructureParams = exports.explodeStructure = exports.unwindStructureAssembly = void 0;
+exports.SpinStructureParams = void 0;
+exports.unwindStructureAssembly = unwindStructureAssembly;
+exports.explodeStructure = explodeStructure;
+exports.getSpinStructureAxisAndOrigin = getSpinStructureAxisAndOrigin;
+exports.spinStructure = spinStructure;
 const param_definition_1 = require("../../mol-util/param-definition");
 const geometry_1 = require("../../mol-math/geometry");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
@@ -19,7 +23,6 @@ function unwindStructureAssembly(structure, unitTransforms, t) {
         unitTransforms.setTransform(_unwindMatrix, u);
     }
 }
-exports.unwindStructureAssembly = unwindStructureAssembly;
 const _centerVec = (0, linear_algebra_1.Vec3)(), _transVec = (0, linear_algebra_1.Vec3)(), _transMat = (0, linear_algebra_1.Mat4)();
 function explodeStructure(structure, unitTransforms, t, sphere) {
     const d = sphere.radius * t;
@@ -32,7 +35,6 @@ function explodeStructure(structure, unitTransforms, t, sphere) {
         unitTransforms.setTransform(_transMat, u);
     }
 }
-exports.explodeStructure = explodeStructure;
 //
 exports.SpinStructureParams = {
     axis: param_definition_1.ParamDefinition.MappedStatic('custom', {
@@ -68,7 +70,6 @@ function getSpinStructureAxisAndOrigin(structure, props) {
     }
     return { axis, origin };
 }
-exports.getSpinStructureAxisAndOrigin = getSpinStructureAxisAndOrigin;
 const _rotMat = (0, linear_algebra_1.Mat4)();
 const _transMat2 = (0, linear_algebra_1.Mat4)();
 const _t = (0, linear_algebra_1.Mat4)();
@@ -84,4 +85,3 @@ function spinStructure(structure, unitTransforms, t, axis, origin) {
         unitTransforms.setTransform(_t, u);
     }
 }
-exports.spinStructure = spinStructure;

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

@@ -6,7 +6,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.PresetTrajectoryHierarchy = exports.TrajectoryHierarchyPresetProvider = void 0;
+exports.PresetTrajectoryHierarchy = void 0;
+exports.TrajectoryHierarchyPresetProvider = TrajectoryHierarchyPresetProvider;
 const param_definition_1 = require("../../../mol-util/param-definition");
 const mol_state_1 = require("../../../mol-state");
 const transforms_1 = require("../../transforms");
@@ -18,7 +19,6 @@ const util_1 = require("../../../mol-repr/util");
 const operator_name_1 = require("../../../mol-theme/color/operator-name");
 const config_1 = require("../../../mol-plugin/config");
 function TrajectoryHierarchyPresetProvider(preset) { return preset; }
-exports.TrajectoryHierarchyPresetProvider = TrajectoryHierarchyPresetProvider;
 (function (TrajectoryHierarchyPresetProvider) {
     TrajectoryHierarchyPresetProvider.CommonParams = (a, plugin) => ({
         modelProperties: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group(mol_state_1.StateTransformer.getParamDefinition(transforms_1.StateTransforms.Model.CustomModelProperties, void 0, plugin))),

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

@@ -6,7 +6,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.PresetStructureRepresentations = exports.presetSelectionComponent = exports.presetStaticComponent = exports.StructureRepresentationPresetProvider = void 0;
+exports.PresetStructureRepresentations = void 0;
+exports.StructureRepresentationPresetProvider = StructureRepresentationPresetProvider;
+exports.presetStaticComponent = presetStaticComponent;
+exports.presetSelectionComponent = presetSelectionComponent;
 const param_definition_1 = require("../../../mol-util/param-definition");
 const base_1 = require("../../../mol-geo/geometry/base");
 const structure_1 = require("../../../mol-model/structure");
@@ -22,7 +25,6 @@ const struct_conn_1 = require("../../../mol-model-formats/structure/property/bon
 const type_helpers_1 = require("../../../mol-util/type-helpers");
 const vec3_1 = require("../../../mol-math/linear-algebra/3d/vec3");
 function StructureRepresentationPresetProvider(repr) { return repr; }
-exports.StructureRepresentationPresetProvider = StructureRepresentationPresetProvider;
 (function (StructureRepresentationPresetProvider) {
     StructureRepresentationPresetProvider.CommonParams = {
         ignoreHydrogens: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false)),
@@ -417,11 +419,9 @@ const autoLod = StructureRepresentationPresetProvider({
 function presetStaticComponent(plugin, structure, type, params) {
     return plugin.builders.structure.tryCreateComponentStatic(structure, type, params);
 }
-exports.presetStaticComponent = presetStaticComponent;
 function presetSelectionComponent(plugin, structure, query, params) {
     return plugin.builders.structure.tryCreateComponentFromSelection(structure, structure_selection_query_1.StructureSelectionQueries[query], `selection-${query}`, params);
 }
-exports.presetSelectionComponent = presetSelectionComponent;
 exports.PresetStructureRepresentations = {
     empty,
     auto,

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

@@ -6,10 +6,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.guessCifVariant = exports.DataFormatProvider = void 0;
+exports.DataFormatProvider = DataFormatProvider;
+exports.guessCifVariant = guessCifVariant;
 const decode_1 = require("../../mol-io/common/msgpack/decode");
 function DataFormatProvider(provider) { return provider; }
-exports.DataFormatProvider = DataFormatProvider;
 function guessCifVariant(info, data) {
     if (info.ext === 'bcif') {
         try {
@@ -37,4 +37,3 @@ function guessCifVariant(info, data) {
     }
     return -1;
 }
-exports.guessCifVariant = guessCifVariant;

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

@@ -25,6 +25,6 @@ export declare class DataFormatRegistry {
     get(name: string): DataFormatProvider | undefined;
     get list(): {
         name: string;
-        provider: DataFormatProvider<any, any, any>;
+        provider: DataFormatProvider;
     }[];
 }

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

@@ -28,39 +28,39 @@ export declare const MolProvider: TrajectoryFormatProvider;
 export declare const SdfProvider: TrajectoryFormatProvider;
 export declare const Mol2Provider: TrajectoryFormatProvider;
 export declare const BuiltInTrajectoryFormats: readonly [readonly ["mmcif", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["cifCore", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["pdb", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["pdbqt", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["gro", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["xyz", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["mol", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["sdf", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>], readonly ["mol2", TrajectoryFormatProvider<{
-    trajectoryTags?: string | string[] | undefined;
+    trajectoryTags?: string | string[];
 }, {
     trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>;
 }>]];

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

@@ -8,7 +8,6 @@
 import { PluginContext } from '../../mol-plugin/context';
 import { StateObjectSelector } from '../../mol-state';
 import { PluginStateObject } from '../objects';
-import { Volume } from '../../mol-model/volume';
 export declare const VolumeFormatCategory = "Volume";
 type Params = {
     entryId?: string;

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

@@ -6,7 +6,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.setStructureClipping = void 0;
+exports.setStructureClipping = setStructureClipping;
 const structure_1 = require("../../mol-model/structure");
 const transforms_1 = require("../../mol-plugin-state/transforms");
 const mol_state_1 = require("../../mol-state");
@@ -39,7 +39,6 @@ async function setStructureClipping(plugin, components, groups, lociGetter, type
         }
     });
 }
-exports.setStructureClipping = setStructureClipping;
 async function eachRepr(plugin, components, callback) {
     const state = plugin.state.data;
     const update = state.build();

package/lib/commonjs/mol-plugin-state/helpers/structure-component.js

@@ -5,7 +5,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.updateStructureComponent = exports.createStructureComponent = exports.StructureComponentParams = exports.StaticStructureComponentTypes = void 0;
+exports.StructureComponentParams = exports.StaticStructureComponentTypes = void 0;
+exports.createStructureComponent = createStructureComponent;
+exports.updateStructureComponent = updateStructureComponent;
 const param_definition_1 = require("../../mol-util/param-definition");
 const builder_1 = require("../../mol-script/language/builder");
 const structure_1 = require("../../mol-model/structure");
@@ -116,7 +118,6 @@ function createStructureComponent(a, params, cache) {
     const props = { label: `${params.label || label || 'Component'}`, description: structure_1.Structure.elementDescription(component) };
     return new objects_1.PluginStateObject.Molecule.Structure(component, props);
 }
-exports.createStructureComponent = createStructureComponent;
 function updateStructureComponent(a, b, oldParams, newParams, cache) {
     if (oldParams.type.name !== newParams.type.name)
         return mol_state_1.StateTransformer.UpdateResult.Recreate;
@@ -181,4 +182,3 @@ function updateStructureComponent(a, b, oldParams, newParams, cache) {
     }
     return updated ? mol_state_1.StateTransformer.UpdateResult.Updated : mol_state_1.StateTransformer.UpdateResult.Unchanged;
 }
-exports.updateStructureComponent = updateStructureComponent;

package/lib/commonjs/mol-plugin-state/helpers/structure-emissive.js

@@ -6,7 +6,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clearStructureEmissive = exports.setStructureEmissive = void 0;
+exports.setStructureEmissive = setStructureEmissive;
+exports.clearStructureEmissive = clearStructureEmissive;
 const structure_1 = require("../../mol-model/structure");
 const transforms_1 = require("../transforms");
 const mol_state_1 = require("../../mol-state");
@@ -39,7 +40,6 @@ async function setStructureEmissive(plugin, components, value, lociGetter, types
         }
     });
 }
-exports.setStructureEmissive = setStructureEmissive;
 async function clearStructureEmissive(plugin, components, types) {
     await eachRepr(plugin, components, async (update, repr, emissiveCell) => {
         if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
@@ -49,7 +49,6 @@ async function clearStructureEmissive(plugin, components, types) {
         }
     });
 }
-exports.clearStructureEmissive = clearStructureEmissive;
 async function eachRepr(plugin, components, callback) {
     const state = plugin.state.data;
     const update = state.build();

package/lib/commonjs/mol-plugin-state/helpers/structure-overpaint.js

@@ -6,7 +6,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clearStructureOverpaint = exports.setStructureOverpaint = void 0;
+exports.setStructureOverpaint = setStructureOverpaint;
+exports.clearStructureOverpaint = clearStructureOverpaint;
 const structure_1 = require("../../mol-model/structure");
 const transforms_1 = require("../../mol-plugin-state/transforms");
 const mol_state_1 = require("../../mol-state");
@@ -41,7 +42,6 @@ async function setStructureOverpaint(plugin, components, color, lociGetter, type
         }
     });
 }
-exports.setStructureOverpaint = setStructureOverpaint;
 async function clearStructureOverpaint(plugin, components, types) {
     await eachRepr(plugin, components, async (update, repr, overpaintCell) => {
         if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
@@ -51,7 +51,6 @@ async function clearStructureOverpaint(plugin, components, types) {
         }
     });
 }
-exports.clearStructureOverpaint = clearStructureOverpaint;
 async function eachRepr(plugin, components, callback) {
     const state = plugin.state.data;
     const update = state.build();

package/lib/commonjs/mol-plugin-state/helpers/structure-representation-params.js

@@ -5,7 +5,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createStructureSizeThemeParams = exports.createStructureColorThemeParams = exports.getStructureThemeTypes = exports.createStructureRepresentationParams = void 0;
+exports.createStructureRepresentationParams = createStructureRepresentationParams;
+exports.getStructureThemeTypes = getStructureThemeTypes;
+exports.createStructureColorThemeParams = createStructureColorThemeParams;
+exports.createStructureSizeThemeParams = createStructureSizeThemeParams;
 const structure_1 = require("../../mol-model/structure");
 const param_definition_1 = require("../../mol-util/param-definition");
 function createStructureRepresentationParams(ctx, structure, props = {}) {
@@ -14,14 +17,12 @@ function createStructureRepresentationParams(ctx, structure, props = {}) {
         return createParamsByName(ctx, structure || structure_1.Structure.Empty, props);
     return createParamsProvider(ctx, structure || structure_1.Structure.Empty, props);
 }
-exports.createStructureRepresentationParams = createStructureRepresentationParams;
 function getStructureThemeTypes(ctx, structure) {
     const { themes: themeCtx } = ctx.representation.structure;
     if (!structure)
         return themeCtx.colorThemeRegistry.types;
     return themeCtx.colorThemeRegistry.getApplicableTypes({ structure });
 }
-exports.getStructureThemeTypes = getStructureThemeTypes;
 function createStructureColorThemeParams(ctx, structure, typeName, themeName, params) {
     const { registry, themes } = ctx.representation.structure;
     const repr = registry.get(typeName || registry.default.name);
@@ -31,7 +32,6 @@ function createStructureColorThemeParams(ctx, structure, typeName, themeName, pa
         Object.assign(colorDefaultParams, repr.defaultColorTheme.props);
     return { name: color.name, params: Object.assign(colorDefaultParams, params) };
 }
-exports.createStructureColorThemeParams = createStructureColorThemeParams;
 function createStructureSizeThemeParams(ctx, structure, typeName, themeName, params) {
     const { registry, themes } = ctx.representation.structure;
     const repr = registry.get(typeName || registry.default.name);
@@ -41,7 +41,6 @@ function createStructureSizeThemeParams(ctx, structure, typeName, themeName, par
         Object.assign(sizeDefaultParams, repr.defaultSizeTheme.props);
     return { name: size.name, params: Object.assign(sizeDefaultParams, params) };
 }
-exports.createStructureSizeThemeParams = createStructureSizeThemeParams;
 function createParamsByName(ctx, structure, props) {
     const typeProvider = (props.type && ctx.representation.structure.registry.get(props.type))
         || ctx.representation.structure.registry.default.provider;

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

@@ -6,7 +6,15 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StructureSelectionQueryRegistry = exports.StructureSelectionQueries = exports.applyBuiltInSelection = exports.getPolymerAndBranchedEntityQueries = exports.getNonStandardResidueQueries = exports.getElementQueries = exports.EntityDescriptionQuery = exports.ElementSymbolQuery = exports.ResidueQuery = exports.StructureSelectionQuery = exports.StructureSelectionCategory = void 0;
+exports.StructureSelectionQueryRegistry = exports.StructureSelectionQueries = exports.StructureSelectionCategory = void 0;
+exports.StructureSelectionQuery = StructureSelectionQuery;
+exports.ResidueQuery = ResidueQuery;
+exports.ElementSymbolQuery = ElementSymbolQuery;
+exports.EntityDescriptionQuery = EntityDescriptionQuery;
+exports.getElementQueries = getElementQueries;
+exports.getNonStandardResidueQueries = getNonStandardResidueQueries;
+exports.getPolymerAndBranchedEntityQueries = getPolymerAndBranchedEntityQueries;
+exports.applyBuiltInSelection = applyBuiltInSelection;
 const structure_1 = require("../../mol-model/structure");
 const types_1 = require("../../mol-model/structure/model/types");
 const builder_1 = require("../../mol-script/language/builder");
@@ -58,7 +66,6 @@ function StructureSelectionQuery(label, expression, props = {}) {
         }
     };
 }
-exports.StructureSelectionQuery = StructureSelectionQuery;
 const all = StructureSelectionQuery('All', builder_1.MolScriptBuilder.struct.generator.all(), { category: '', priority: 1000 });
 const current = StructureSelectionQuery('Current Selection', builder_1.MolScriptBuilder.internal.generator.current(), { category: '', referencesCurrent: true });
 const polymer = StructureSelectionQuery('Polymer', builder_1.MolScriptBuilder.struct.modifier.union([
@@ -560,7 +567,6 @@ function ResidueQuery([names, label], category, priority = 0) {
         })
     ]), { category, priority, description });
 }
-exports.ResidueQuery = ResidueQuery;
 function ElementSymbolQuery([names, label], category, priority) {
     const description = `${label} (${names.join(', ')})`;
     return StructureSelectionQuery(description, builder_1.MolScriptBuilder.struct.modifier.union([
@@ -569,7 +575,6 @@ function ElementSymbolQuery([names, label], category, priority) {
         })
     ]), { category, priority, description });
 }
-exports.ElementSymbolQuery = ElementSymbolQuery;
 function EntityDescriptionQuery([names, label], category, priority) {
     const description = `${label}`;
     return StructureSelectionQuery(`${label}`, builder_1.MolScriptBuilder.struct.modifier.union([
@@ -578,7 +583,6 @@ function EntityDescriptionQuery([names, label], category, priority) {
         })
     ]), { category, priority, description });
 }
-exports.EntityDescriptionQuery = EntityDescriptionQuery;
 const StandardResidues = set_1.SetUtils.unionMany(types_1.AminoAcidNamesL, types_1.RnaBaseNames, types_1.DnaBaseNames, types_1.WaterNames);
 function getElementQueries(structures) {
     const uniqueElements = new Set();
@@ -592,7 +596,6 @@ function getElementQueries(structures) {
     });
     return queries;
 }
-exports.getElementQueries = getElementQueries;
 function getNonStandardResidueQueries(structures) {
     const residueLabels = new Map();
     const uniqueResidues = new Set();
@@ -613,7 +616,6 @@ function getNonStandardResidueQueries(structures) {
     });
     return queries;
 }
-exports.getNonStandardResidueQueries = getNonStandardResidueQueries;
 function getPolymerAndBranchedEntityQueries(structures) {
     const uniqueEntities = new Map();
     const l = structure_1.StructureElement.Location.create();
@@ -635,11 +637,9 @@ function getPolymerAndBranchedEntityQueries(structures) {
     });
     return queries;
 }
-exports.getPolymerAndBranchedEntityQueries = getPolymerAndBranchedEntityQueries;
 function applyBuiltInSelection(to, query, customTag) {
     return to.apply(transforms_1.StateTransforms.Model.StructureSelectionFromExpression, { expression: exports.StructureSelectionQueries[query].expression, label: exports.StructureSelectionQueries[query].label }, { tags: customTag ? [query, customTag] : [query] });
 }
-exports.applyBuiltInSelection = applyBuiltInSelection;
 exports.StructureSelectionQueries = {
     all,
     current,

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

@@ -6,7 +6,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clearStructureSubstance = exports.setStructureSubstance = void 0;
+exports.setStructureSubstance = setStructureSubstance;
+exports.clearStructureSubstance = clearStructureSubstance;
 const structure_1 = require("../../mol-model/structure");
 const transforms_1 = require("../../mol-plugin-state/transforms");
 const mol_state_1 = require("../../mol-state");
@@ -41,7 +42,6 @@ async function setStructureSubstance(plugin, components, material, lociGetter, t
         }
     });
 }
-exports.setStructureSubstance = setStructureSubstance;
 async function clearStructureSubstance(plugin, components, types) {
     await eachRepr(plugin, components, async (update, repr, substanceCell) => {
         if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
@@ -51,7 +51,6 @@ async function clearStructureSubstance(plugin, components, types) {
         }
     });
 }
-exports.clearStructureSubstance = clearStructureSubstance;
 async function eachRepr(plugin, components, callback) {
     const state = plugin.state.data;
     const update = state.build();

package/lib/commonjs/mol-plugin-state/helpers/structure-transparency.js

@@ -6,7 +6,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clearStructureTransparency = exports.setStructureTransparency = void 0;
+exports.setStructureTransparency = setStructureTransparency;
+exports.clearStructureTransparency = clearStructureTransparency;
 const structure_1 = require("../../mol-model/structure");
 const transforms_1 = require("../../mol-plugin-state/transforms");
 const mol_state_1 = require("../../mol-state");
@@ -39,7 +40,6 @@ async function setStructureTransparency(plugin, components, value, lociGetter, t
         }
     });
 }
-exports.setStructureTransparency = setStructureTransparency;
 async function clearStructureTransparency(plugin, components, types) {
     await eachRepr(plugin, components, async (update, repr, transparencyCell) => {
         if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
@@ -49,7 +49,6 @@ async function clearStructureTransparency(plugin, components, types) {
         }
     });
 }
-exports.clearStructureTransparency = clearStructureTransparency;
 async function eachRepr(plugin, components, callback) {
     const state = plugin.state.data;
     const update = state.build();

package/lib/commonjs/mol-plugin-state/helpers/volume-representation-params.js

@@ -5,7 +5,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createVolumeSizeThemeParams = exports.createVolumeColorThemeParams = exports.getVolumeThemeTypes = exports.createVolumeRepresentationParams = void 0;
+exports.createVolumeRepresentationParams = createVolumeRepresentationParams;
+exports.getVolumeThemeTypes = getVolumeThemeTypes;
+exports.createVolumeColorThemeParams = createVolumeColorThemeParams;
+exports.createVolumeSizeThemeParams = createVolumeSizeThemeParams;
 const volume_1 = require("../../mol-model/volume");
 const param_definition_1 = require("../../mol-util/param-definition");
 function createVolumeRepresentationParams(ctx, volume, props = {}) {
@@ -14,14 +17,12 @@ function createVolumeRepresentationParams(ctx, volume, props = {}) {
         return createParamsByName(ctx, volume || volume_1.Volume.One, props);
     return createParamsProvider(ctx, volume || volume_1.Volume.One, props);
 }
-exports.createVolumeRepresentationParams = createVolumeRepresentationParams;
 function getVolumeThemeTypes(ctx, volume) {
     const { themes: themeCtx } = ctx.representation.volume;
     if (!volume)
         return themeCtx.colorThemeRegistry.types;
     return themeCtx.colorThemeRegistry.getApplicableTypes({ volume });
 }
-exports.getVolumeThemeTypes = getVolumeThemeTypes;
 function createVolumeColorThemeParams(ctx, volume, typeName, themeName, params) {
     const { registry, themes } = ctx.representation.volume;
     const repr = registry.get(typeName || registry.default.name);
@@ -31,7 +32,6 @@ function createVolumeColorThemeParams(ctx, volume, typeName, themeName, params)
         Object.assign(colorDefaultParams, repr.defaultColorTheme.props);
     return { name: color.name, params: Object.assign(colorDefaultParams, params) };
 }
-exports.createVolumeColorThemeParams = createVolumeColorThemeParams;
 function createVolumeSizeThemeParams(ctx, volume, typeName, themeName, params) {
     const { registry, themes } = ctx.representation.volume;
     const repr = registry.get(typeName || registry.default.name);
@@ -41,7 +41,6 @@ function createVolumeSizeThemeParams(ctx, volume, typeName, themeName, params) {
         Object.assign(sizeDefaultParams, repr.defaultSizeTheme.props);
     return { name: size.name, params: Object.assign(sizeDefaultParams, params) };
 }
-exports.createVolumeSizeThemeParams = createVolumeSizeThemeParams;
 function createParamsByName(ctx, volume, props) {
     const typeProvider = (props.type && ctx.representation.volume.registry.get(props.type))
         || ctx.representation.volume.registry.default.provider;

package/lib/commonjs/mol-plugin-state/manager/focus-camera/focus-first-residue.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getPcaTransform = exports.pcaFocus = void 0;
+exports.pcaFocus = pcaFocus;
+exports.getPcaTransform = getPcaTransform;
 const vec3_1 = require("../../..//mol-math/linear-algebra/3d/vec3");
 const principal_axes_1 = require("../../../mol-math/linear-algebra/matrix/principal-axes");
 const camera_1 = require("../../../mol-canvas3d/camera");
@@ -97,7 +98,6 @@ function pcaFocus(plugin, radius, options) {
     }
     return plugin.canvas3d.camera.getFocus(origin, radius, up, dir, camera_1.Camera.createDefaultSnapshot());
 }
-exports.pcaFocus = pcaFocus;
 function getPcaTransform(group) {
     var _a;
     const structure = (_a = group[0].cell.obj) === null || _a === void 0 ? void 0 : _a.data;
@@ -119,4 +119,3 @@ function getPcaTransform(group) {
     structure.currentPropertyData._pcaTransformData = pcaTransfromData;
     return pcaTransfromData;
 }
-exports.getPcaTransform = getPcaTransform;

package/lib/commonjs/mol-plugin-state/manager/focus-camera/orient-axes.js

@@ -5,7 +5,10 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.changeCameraRotation = exports.layingTransform = exports.structureLayingTransform = exports.ROTATION_MATRICES = void 0;
+exports.ROTATION_MATRICES = void 0;
+exports.structureLayingTransform = structureLayingTransform;
+exports.layingTransform = layingTransform;
+exports.changeCameraRotation = changeCameraRotation;
 const linear_algebra_1 = require("../../../mol-math/linear-algebra");
 const principal_axes_1 = require("../../../mol-math/linear-algebra/matrix/principal-axes");
 const structure_1 = require("../../../mol-model/structure");
@@ -38,7 +41,6 @@ function structureLayingTransform(structures, referenceRotation) {
     const coords = smartSelectCoords(structures, MIN_ATOMS_FOR_PCA);
     return layingTransform(coords, referenceRotation);
 }
-exports.structureLayingTransform = structureLayingTransform;
 /** Return transformation which will align the PCA axes of a sequence
  * of points to the Cartesian axes x, y, z
  * (transformed = rotation * (coords - origin)).
@@ -62,7 +64,6 @@ function layingTransform(coords, referenceRotation) {
     linear_algebra_1.Mat3.mul(R, flip, R);
     return { rotation: R, origin: normAxes.origin };
 }
-exports.layingTransform = layingTransform;
 /** Try these selection strategies until having at least `minAtoms` atoms:
  * 1. only trace atoms (e.g. C-alpha and O3')
  * 2. all non-hydrogen atoms with exception of water (HOH)
@@ -213,4 +214,3 @@ function changeCameraRotation(old, rotation) {
     const newPosition = linear_algebra_1.Vec3.add((0, linear_algebra_1.Vec3)(), old.target, relPosition);
     return { ...old, position: newPosition, up: newUp };
 }
-exports.changeCameraRotation = changeCameraRotation;