molstar 4.2.0 → 4.4.0

package/lib/commonjs/apps/viewer/app.js

@@ -4,6 +4,7 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Neli Fonseca <neli@ebi.ac.uk>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PluginExtensions = exports.ViewerAutoPreset = exports.Viewer = exports.ExtensionMap = exports.setTimingMode = exports.setProductionMode = exports.setDebugMode = exports.consoleStats = exports.version = void 0;
@@ -44,6 +45,7 @@ const spec_2 = require("../../mol-plugin/spec");
 const mol_state_1 = require("../../mol-state");
 const mol_task_1 = require("../../mol-task");
 const assets_1 = require("../../mol-util/assets");
+const color_1 = require("../../mol-util/color");
 require("../../mol-util/polyfill");
 const type_helpers_1 = require("../../mol-util/type-helpers");
 var version_1 = require("../../mol-plugin/version");
@@ -73,6 +75,7 @@ exports.ExtensionMap = {
     'sb-ncbr-partial-charges': spec_2.PluginSpec.Behavior(sb_ncbr_1.SbNcbrPartialCharges),
     'wwpdb-chemical-component-dictionary': spec_2.PluginSpec.Behavior(behavior_4.wwPDBChemicalComponentDictionary),
     'mvs': spec_2.PluginSpec.Behavior(behavior_3.MolViewSpec),
+    'tunnels': spec_2.PluginSpec.Behavior(sb_ncbr_1.SbNcbrTunnels),
 };
 const DefaultViewerOptions = {
     customFormats: CustomFormats,
@@ -392,6 +395,32 @@ class Viewer {
             await repr.commit();
         });
     }
+    loadFullResolutionEMDBMap(emdbId, options) {
+        const plugin = this.plugin;
+        const numericId = parseInt(emdbId.toUpperCase().replace('EMD-', ''));
+        const url = `https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-${numericId}/map/emd_${numericId}.map.gz`;
+        return plugin.dataTransaction(async () => {
+            var _a, _b, _c;
+            const data = await plugin.build().toRoot()
+                .apply(transforms_1.StateTransforms.Data.Download, { url, isBinary: true, label: emdbId }, { state: { isGhost: true } })
+                .apply(transforms_1.StateTransforms.Data.DeflateData)
+                .commit();
+            const parsed = await plugin.dataFormats.get('ccp4').parse(plugin, data, { entryId: emdbId });
+            const firstVolume = (parsed.volume || parsed.volumes[0]);
+            if (!(firstVolume === null || firstVolume === void 0 ? void 0 : firstVolume.isOk))
+                throw new Error('Failed to parse any volume.');
+            const volume = (_b = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[0]) !== null && _b !== void 0 ? _b : parsed.volume;
+            await plugin.build()
+                .to(volume)
+                .apply(transforms_1.StateTransforms.Representation.VolumeRepresentation3D, (0, volume_representation_params_1.createVolumeRepresentationParams)(this.plugin, firstVolume.data, {
+                type: 'isosurface',
+                typeParams: { alpha: 1, isoValue: options.isoValue },
+                color: 'uniform',
+                colorParams: { value: (_c = options.color) !== null && _c !== void 0 ? _c : (0, color_1.Color)(0x33BB33) }
+            }))
+                .commit();
+        });
+    }
     /**
      * @example
      *  viewer.loadTrajectory({

package/lib/commonjs/cli/chem-comp-dict/util.js

@@ -5,7 +5,13 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DefaultDataOptions = exports.getEncodedCif = exports.readPVCD = exports.readCCD = exports.readFileAsCollection = exports.ensureDataAvailable = exports.ensureAvailable = void 0;
+exports.DefaultDataOptions = void 0;
+exports.ensureAvailable = ensureAvailable;
+exports.ensureDataAvailable = ensureDataAvailable;
+exports.readFileAsCollection = readFileAsCollection;
+exports.readCCD = readCCD;
+exports.readPVCD = readPVCD;
+exports.getEncodedCif = getEncodedCif;
 const tslib_1 = require("tslib");
 const util = tslib_1.__importStar(require("util"));
 const path = tslib_1.__importStar(require("path"));
@@ -35,25 +41,20 @@ async function ensureAvailable(path, url, forceDownload = false) {
         console.log(`done downloading ${url}`);
     }
 }
-exports.ensureAvailable = ensureAvailable;
 async function ensureDataAvailable(options) {
     await ensureAvailable(CCD_PATH, options.ccdUrl || CCD_URL, !!options.ccdUrl || options.forceDownload);
     await ensureAvailable(PVCD_PATH, options.pvcdUrl || PVCD_URL, !!options.pvcdUrl || options.forceDownload);
 }
-exports.ensureDataAvailable = ensureDataAvailable;
 async function readFileAsCollection(path, schema) {
     const parsed = await parseCif(await readFile(path, 'utf8'));
     return cif_1.CIF.toDatabaseCollection(schema, parsed.result);
 }
-exports.readFileAsCollection = readFileAsCollection;
 async function readCCD() {
     return readFileAsCollection(CCD_PATH, ccd_1.CCD_Schema);
 }
-exports.readCCD = readCCD;
 async function readPVCD() {
     return readFileAsCollection(PVCD_PATH, ccd_1.CCD_Schema);
 }
-exports.readPVCD = readPVCD;
 async function parseCif(data) {
     const comp = cif_1.CIF.parse(data);
     console.time('parse cif');
@@ -68,7 +69,6 @@ function getEncodedCif(name, database, binary = false) {
     cif_2.CifWriter.Encoder.writeDatabase(encoder, name, database);
     return encoder.getData();
 }
-exports.getEncodedCif = getEncodedCif;
 exports.DefaultDataOptions = {
     forceDownload: false
 };

package/lib/commonjs/cli/cif2bcif/converter.js

@@ -6,7 +6,7 @@
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.convert = void 0;
+exports.convert = convert;
 const tslib_1 = require("tslib");
 const cif_1 = require("../../mol-io/reader/cif");
 const cif_2 = require("../../mol-io/writer/cif");
@@ -114,4 +114,3 @@ function convert(path, asText = false, hints, filter) {
         return ret;
     }).run(showProgress, 250);
 }
-exports.convert = convert;

package/lib/commonjs/cli/cifschema/util/cif-dic.js

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.generateSchema = exports.getFieldType = void 0;
+exports.getFieldType = getFieldType;
+exports.generateSchema = generateSchema;
 const schema_1 = require("./schema");
 const helper_1 = require("./helper");
 function getFieldType(type, description, values, container) {
@@ -100,7 +101,6 @@ function getFieldType(type, description, values, container) {
     console.log(`unknown type '${type}'`);
     return (0, schema_1.StrCol)(description);
 }
-exports.getFieldType = getFieldType;
 function ColFromType(type, description) {
     switch (type) {
         case 'int': return (0, schema_1.IntCol)(description);
@@ -452,4 +452,3 @@ function generateSchema(frames, imports = new Map()) {
     });
     return { tables, aliases };
 }
-exports.generateSchema = generateSchema;

package/lib/commonjs/cli/cifschema/util/generate.js

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.generate = void 0;
+exports.generate = generate;
 const string_1 = require("../../../mol-util/string");
 const schema_1 = require("../../../mol-io/reader/cif/schema");
 function header(name, info, moldataImportPath) {
@@ -175,4 +175,3 @@ function generate(name, info, schema, fields, moldataImportPath, addAliases) {
     }
     return `${header(name, info, moldataImportPath)}\n\n${getTypeShorthands(schema, fields)}\n\n${codeLines.join('\n')}\n${footer(name)}`;
 }
-exports.generate = generate;

package/lib/commonjs/cli/cifschema/util/helper.js

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseImportGet = void 0;
+exports.parseImportGet = parseImportGet;
 function parseImportGet(s) {
     // [{'save':hi_ang_Fox_coeffs  'file':templ_attr.cif}   {'save':hi_ang_Fox_c0  'file':templ_enum.cif}]
     // [{"file":'templ_enum.cif' "save":'H_M_ref'}]
@@ -18,4 +18,3 @@ function parseImportGet(s) {
         };
     });
 }
-exports.parseImportGet = parseImportGet;

package/lib/commonjs/cli/cifschema/util/schema.js

@@ -5,31 +5,31 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.mergeFilters = exports.ListCol = exports.MatrixCol = exports.VectorCol = exports.EnumCol = exports.CoordCol = exports.FloatCol = exports.StrCol = exports.IntCol = void 0;
-function IntCol(description) { return { type: 'int', description }; }
 exports.IntCol = IntCol;
-function StrCol(description) { return { type: 'str', description }; }
 exports.StrCol = StrCol;
-function FloatCol(description) { return { type: 'float', description }; }
 exports.FloatCol = FloatCol;
-function CoordCol(description) { return { type: 'coord', description }; }
 exports.CoordCol = CoordCol;
+exports.EnumCol = EnumCol;
+exports.VectorCol = VectorCol;
+exports.MatrixCol = MatrixCol;
+exports.ListCol = ListCol;
+exports.mergeFilters = mergeFilters;
+function IntCol(description) { return { type: 'int', description }; }
+function StrCol(description) { return { type: 'str', description }; }
+function FloatCol(description) { return { type: 'float', description }; }
+function CoordCol(description) { return { type: 'coord', description }; }
 function EnumCol(values, subType, description) {
     return { type: 'enum', description, values, subType };
 }
-exports.EnumCol = EnumCol;
 function VectorCol(length, description) {
     return { type: 'vector', description, length };
 }
-exports.VectorCol = VectorCol;
 function MatrixCol(columns, rows, description) {
     return { type: 'matrix', description, columns, rows };
 }
-exports.MatrixCol = MatrixCol;
 function ListCol(subType, separator, description) {
     return { type: 'list', description, separator, subType };
 }
-exports.ListCol = ListCol;
 function mergeFilters(...filters) {
     const n = filters.length;
     const mergedFilter = {};
@@ -56,4 +56,3 @@ function mergeFilters(...filters) {
     });
     return mergedFilter;
 }
-exports.mergeFilters = mergeFilters;

package/lib/commonjs/cli/state-docs/pd-to-md.js

@@ -5,12 +5,11 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.paramsToMd = void 0;
+exports.paramsToMd = paramsToMd;
 const param_definition_1 = require("../../mol-util/param-definition");
 function paramsToMd(params) {
     return getParams(params, 0);
 }
-exports.paramsToMd = paramsToMd;
 function paramInfo(param, offset) {
     switch (param.type) {
         case 'value': return 'Value';

package/lib/commonjs/cli/structure-info/helpers.js

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.downloadCif = exports.openCif = void 0;
+exports.openCif = openCif;
+exports.downloadCif = downloadCif;
 const tslib_1 = require("tslib");
 const util = tslib_1.__importStar(require("util"));
 const fs = tslib_1.__importStar(require("fs"));
@@ -37,9 +38,7 @@ async function openCif(path) {
     const data = await readFile(path);
     return parseCif(data);
 }
-exports.openCif = openCif;
 async function downloadCif(url, isBinary) {
     const data = await (0, node_fetch_1.default)(url);
     return parseCif(isBinary ? new Uint8Array(await data.arrayBuffer()) : await data.text());
 }
-exports.downloadCif = downloadCif;

package/lib/commonjs/cli/structure-info/model.js

@@ -7,7 +7,17 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getModelsAndStructure = exports.printModelStats = exports.printSymmetryInfo = exports.printUnits = exports.printRings = exports.printSequence = exports.printBonds = exports.printSecStructure = exports.residueLabel = exports.atomLabel = exports.readCifFile = void 0;
+exports.readCifFile = readCifFile;
+exports.atomLabel = atomLabel;
+exports.residueLabel = residueLabel;
+exports.printSecStructure = printSecStructure;
+exports.printBonds = printBonds;
+exports.printSequence = printSequence;
+exports.printRings = printRings;
+exports.printUnits = printUnits;
+exports.printSymmetryInfo = printSymmetryInfo;
+exports.printModelStats = printModelStats;
+exports.getModelsAndStructure = getModelsAndStructure;
 const tslib_1 = require("tslib");
 const argparse = tslib_1.__importStar(require("argparse"));
 require('util.promisify').shim();
@@ -30,7 +40,6 @@ async function readCifFile(path) {
     const parsed = await (0, helpers_1.openCif)(path);
     return parsed.blocks[0];
 }
-exports.readCifFile = readCifFile;
 function atomLabel(model, aI) {
     const { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
     const { label_atom_id, label_comp_id } = atoms;
@@ -40,7 +49,6 @@ function atomLabel(model, aI) {
     const cI = chainAtomSegments.index[aI];
     return `${label_asym_id.value(cI)} ${label_comp_id.value(aI)} ${label_seq_id.value(rI)} ${label_atom_id.value(aI)}`;
 }
-exports.atomLabel = atomLabel;
 function residueLabel(model, rI) {
     const { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
     const { label_comp_id } = atoms;
@@ -50,7 +58,6 @@ function residueLabel(model, rI) {
     const cI = chainAtomSegments.index[aI];
     return `${label_asym_id.value(cI)} ${label_comp_id.value(aI)} ${label_seq_id.value(rI)}`;
 }
-exports.residueLabel = residueLabel;
 function printSecStructure(model) {
     console.log('\nSecondary Structure\n=============');
     const { residues } = model.atomicHierarchy;
@@ -71,7 +78,6 @@ function printSecStructure(model) {
         rI++;
     }
 }
-exports.printSecStructure = printSecStructure;
 function printBonds(structure, showIntra, showInter) {
     if (showIntra) {
         console.log('\nIntra Unit Bonds\n=============');
@@ -113,7 +119,6 @@ function printBonds(structure, showIntra, showInter) {
         }
     }
 }
-exports.printBonds = printBonds;
 function printSequence(model) {
     console.log('\nSequence\n=============');
     const { byEntityKey } = model.sequence;
@@ -125,7 +130,6 @@ function printSequence(model) {
     }
     console.log();
 }
-exports.printSequence = printSequence;
 function printRings(structure) {
     console.log('\nRings\n=============');
     for (const unit of structure.units) {
@@ -142,7 +146,6 @@ function printRings(structure) {
     }
     console.log();
 }
-exports.printRings = printRings;
 function printUnits(structure) {
     console.log('\nUnits\n=============');
     const l = structure_1.StructureElement.Location.create(structure);
@@ -171,7 +174,6 @@ function printUnits(structure) {
         }
     }
 }
-exports.printUnits = printUnits;
 function printSymmetryInfo(model) {
     console.log('\nSymmetry Info\n=============');
     const symmetry = symmetry_1.ModelSymmetry.Provider.get(model);
@@ -183,7 +185,6 @@ function printSymmetryInfo(model) {
     // NCS example: 1auy
     console.log(`NCS operators: ${symmetry.ncsOperators && symmetry.ncsOperators.map(a => a.name).join(', ')}`);
 }
-exports.printSymmetryInfo = printSymmetryInfo;
 async function printModelStats(models) {
     console.log('\nModels\n=============');
     for (let i = 0; i < models.frameCount; i++) {
@@ -197,13 +198,11 @@ async function printModelStats(models) {
     }
     console.log();
 }
-exports.printModelStats = printModelStats;
 async function getModelsAndStructure(frame) {
     const models = await (0, mmcif_1.trajectoryFromMmCIF)(frame).run();
     const structure = structure_1.Structure.ofModel(models.representative);
     return { models, structure };
 }
-exports.getModelsAndStructure = getModelsAndStructure;
 async function run(frame, args) {
     const { models, structure } = await getModelsAndStructure(frame);
     if (args.models)

package/lib/commonjs/examples/alpha-orbitals/controls.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.mountControls = void 0;
+exports.mountControls = mountControls;
 const jsx_runtime_1 = require("react/jsx-runtime");
 /**
  * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
@@ -14,7 +14,6 @@ const plugin_1 = require("../../mol-plugin-ui/plugin");
 function mountControls(orbitals, parent) {
     (0, client_1.createRoot)(parent).render((0, jsx_runtime_1.jsx)(plugin_1.PluginContextContainer, { plugin: orbitals.plugin, children: (0, jsx_runtime_1.jsx)(Controls, { orbitals: orbitals }) }));
 }
-exports.mountControls = mountControls;
 function Controls({ orbitals }) {
     const params = (0, use_behavior_1.useBehavior)(orbitals.params);
     const values = (0, use_behavior_1.useBehavior)(orbitals.state);

package/lib/commonjs/examples/basic-wrapper/custom-theme.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CustomColorThemeProvider = exports.CustomColorTheme = void 0;
+exports.CustomColorThemeProvider = void 0;
+exports.CustomColorTheme = CustomColorTheme;
 const location_iterator_1 = require("../../mol-geo/util/location-iterator");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const color_1 = require("../../mol-theme/color");
@@ -36,7 +37,6 @@ function CustomColorTheme(ctx, props) {
         description: '',
     };
 }
-exports.CustomColorTheme = CustomColorTheme;
 exports.CustomColorThemeProvider = {
     name: 'basic-wrapper-custom-color-theme',
     label: 'Custom Color Theme',

package/lib/commonjs/examples/basic-wrapper/superposition.js

@@ -5,7 +5,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.dynamicSuperpositionTest = exports.StaticSuperpositionTestData = exports.buildStaticSuperposition = void 0;
+exports.StaticSuperpositionTestData = void 0;
+exports.buildStaticSuperposition = buildStaticSuperposition;
+exports.dynamicSuperpositionTest = dynamicSuperpositionTest;
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const structure_1 = require("../../mol-model/structure");
 const superposition_1 = require("../../mol-model/structure/structure/util/superposition");
@@ -24,7 +26,6 @@ function buildStaticSuperposition(plugin, src) {
         }
     });
 }
-exports.buildStaticSuperposition = buildStaticSuperposition;
 exports.StaticSuperpositionTestData = [
     {
         pdbId: '1aj5', auth_asym_id: 'A', matrix: linear_algebra_1.Mat4.identity()
@@ -75,7 +76,6 @@ function dynamicSuperpositionTest(plugin, src, comp_id) {
         }
     });
 }
-exports.dynamicSuperpositionTest = dynamicSuperpositionTest;
 async function siteVisual(plugin, s, pivot, rest) {
     const center = await plugin.builders.structure.tryCreateComponentFromExpression(s, pivot, 'pivot');
     if (center)

package/lib/commonjs/examples/domain-annotation-server/mapping.js

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createMapping = void 0;
+exports.createMapping = createMapping;
 const tslib_1 = require("tslib");
 const db_1 = require("../../mol-data/db");
 const cif_1 = require("../../mol-io/writer/cif");
@@ -27,7 +27,6 @@ function createMapping(allData) {
     }
     return enc.getData();
 }
-exports.createMapping = createMapping;
 function writeDomain(enc, domain) {
     if (!domain)
         return;

package/lib/commonjs/examples/lighting/index.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2023 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/examples/lighting/index.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2023 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -25,6 +25,7 @@ const Canvas3DPresets = {
                         radius: 5,
                         bias: 0.8,
                         blurKernelSize: 15,
+                        blurDepthBias: 0.5,
                         resolutionScale: 1,
                         color: (0, color_1.Color)(0x000000),
                     }

package/lib/commonjs/examples/proteopedia-wrapper/coloring.d.ts

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { Color } from '../../mol-util/color';
-import { ColorTheme, LocationColor } from '../../mol-theme/color';
+import { ColorTheme } from '../../mol-theme/color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../../mol-theme/theme';
 export declare function createProteopediaCustomTheme(colors: number[]): {
@@ -16,26 +16,11 @@ export declare function createProteopediaCustomTheme(colors: number[]): {
         colors: PD.ObjectList<PD.Normalize<{
             color: Color;
         }>>;
-    }>) => {
-        readonly granularity: import("../../mol-geo/geometry/color-data").ColorTypeLocation;
-        readonly color: LocationColor;
-    } & {
-        readonly factory: ColorTheme.Factory<{
-            colors: PD.ObjectList<PD.Normalize<{
-                color: Color;
-            }>>;
-        }, import("../../mol-geo/geometry/color-data").ColorTypeLocation>;
-        readonly props: Readonly<PD.Values<{
-            colors: PD.ObjectList<PD.Normalize<{
-                color: Color;
-            }>>;
+    }>) => ColorTheme<{
+        colors: PD.ObjectList<PD.Normalize<{
+            color: Color;
         }>>;
-        readonly palette?: Readonly<ColorTheme.Palette> | undefined;
-        readonly preferSmoothing?: boolean | undefined;
-        readonly contextHash?: number | undefined;
-        readonly description?: string | undefined;
-        readonly legend?: Readonly<import("../../mol-util/legend").TableLegend | import("../../mol-util/legend").ScaleLegend> | undefined;
-    };
+    }>;
     getParams: (ctx: ThemeDataContext) => {
         colors: PD.ObjectList<PD.Normalize<{
             color: Color;

package/lib/commonjs/examples/proteopedia-wrapper/coloring.js

@@ -6,7 +6,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createProteopediaCustomTheme = void 0;
+exports.createProteopediaCustomTheme = createProteopediaCustomTheme;
 const structure_1 = require("../../mol-model/structure");
 const color_1 = require("../../mol-util/color");
 const param_definition_1 = require("../../mol-util/param-definition");
@@ -90,4 +90,3 @@ function createProteopediaCustomTheme(colors) {
         isApplicable: (ctx) => !!ctx.structure
     };
 }
-exports.createProteopediaCustomTheme = createProteopediaCustomTheme;

package/lib/commonjs/examples/proteopedia-wrapper/ui/controls.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.volumeStreamingControls = void 0;
+exports.volumeStreamingControls = volumeStreamingControls;
 const tslib_1 = require("tslib");
 const jsx_runtime_1 = require("react/jsx-runtime");
 /**
@@ -15,4 +15,3 @@ const helpers_1 = require("../helpers");
 function volumeStreamingControls(plugin, parent) {
     ReactDOM.render((0, jsx_runtime_1.jsx)(plugin_1.PluginContextContainer, { plugin: plugin, children: (0, jsx_runtime_1.jsx)(update_transform_1.TransformUpdaterControl, { nodeRef: helpers_1.StateElements.VolumeStreaming }) }), parent);
 }
-exports.volumeStreamingControls = volumeStreamingControls;

package/lib/commonjs/examples/task.js

@@ -5,7 +5,12 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.logP = exports.abortingObserver = exports.ms = exports.testTree = exports.abortAfter = exports.test1 = void 0;
+exports.ms = void 0;
+exports.test1 = test1;
+exports.abortAfter = abortAfter;
+exports.testTree = testTree;
+exports.abortingObserver = abortingObserver;
+exports.logP = logP;
 const mol_task_1 = require("../mol-task");
 const now_1 = require("../mol-util/now");
 async function test1() {
@@ -13,7 +18,6 @@ async function test1() {
     const r = await t.run();
     console.log(r);
 }
-exports.test1 = test1;
 function messageTree(root, prefix = '') {
     const p = root.progress;
     if (!root.children.length) {
@@ -44,7 +48,6 @@ function abortAfter(delay) {
         // return r;
     });
 }
-exports.abortAfter = abortAfter;
 function testTree() {
     return mol_task_1.Task.create('test o', async (ctx) => {
         await mol_task_1.Scheduler.delay(250);
@@ -67,7 +70,6 @@ function testTree() {
         return r + 1;
     }, () => console.log('On abort O'));
 }
-exports.testTree = testTree;
 function processChunk(n, state) {
     const toProcess = Math.min(state.current + n, state.total);
     const start = state.current;
@@ -101,9 +103,7 @@ function abortingObserver(p) {
         p.requestAbort('test');
     }
 }
-exports.abortingObserver = abortingObserver;
 function logP(p) { console.log(messageTree(p.root)); }
-exports.logP = logP;
 async function test() {
     try {
         // const r = await Run(testTree(), p => console.log(messageTree(p.root)), 250);

package/lib/commonjs/extensions/alpha-orbitals/collocation.js

@@ -7,7 +7,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.sphericalCollocation = void 0;
+exports.sphericalCollocation = sphericalCollocation;
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const array_1 = require("../../mol-util/array");
 const spherical_functions_1 = require("./spherical-functions");
@@ -47,7 +47,6 @@ async function sphericalCollocation(grid, orbital, taskCtx) {
     }
     return matrix;
 }
-exports.sphericalCollocation = sphericalCollocation;
 function collocationBasis(matrix, grid, L, coefficients, exponents, center, cutoffThreshold, alpha) {
     const ncoeff = exponents.length;
     const sphericalFunc = spherical_functions_1.SphericalFunctions[L];

package/lib/commonjs/extensions/alpha-orbitals/data-model.js

@@ -5,7 +5,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createGrid = exports.initCubeGrid = exports.isCubeGridData = exports.CubeGridFormat = void 0;
+exports.CubeGridFormat = CubeGridFormat;
+exports.isCubeGridData = isCubeGridData;
+exports.initCubeGrid = initCubeGrid;
+exports.createGrid = createGrid;
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const geometry_1 = require("../../mol-math/geometry");
 const array_1 = require("../../mol-util/array");
@@ -13,11 +16,9 @@ const array_1 = require("../../mol-util/array");
 function CubeGridFormat(grid) {
     return { name: 'custom grid', kind: 'cube-grid', data: grid };
 }
-exports.CubeGridFormat = CubeGridFormat;
 function isCubeGridData(f) {
     return f.kind === 'cube-grid';
 }
-exports.isCubeGridData = isCubeGridData;
 function initCubeGrid(params) {
     const geometry = params.basis.atoms.map(a => a.center);
     const { gridSpacing: spacing, boxExpand: expand } = params;
@@ -42,7 +43,6 @@ function initCubeGrid(params) {
         delta: linear_algebra_1.Vec3.div((0, linear_algebra_1.Vec3)(), size, linear_algebra_1.Vec3.subScalar((0, linear_algebra_1.Vec3)(), dimensions, 1)),
     };
 }
-exports.initCubeGrid = initCubeGrid;
 const BohrToAngstromFactor = 0.529177210859;
 function createGrid(gridInfo, values, axisOrder) {
     const boxSize = geometry_1.Box3D.size((0, linear_algebra_1.Vec3)(), gridInfo.box);
@@ -64,4 +64,3 @@ function createGrid(gridInfo, values, axisOrder) {
     };
     return grid;
 }
-exports.createGrid = createGrid;

package/lib/commonjs/extensions/alpha-orbitals/density.js

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.computeDensityIsocontourValues = exports.createSphericalCollocationDensityGrid = void 0;
+exports.createSphericalCollocationDensityGrid = createSphericalCollocationDensityGrid;
+exports.computeDensityIsocontourValues = computeDensityIsocontourValues;
 const util_1 = require("../../mol-data/util");
 const grid3d_1 = require("../../mol-gl/compute/grid3d");
 const mol_task_1 = require("../../mol-task");
@@ -34,7 +35,6 @@ function createSphericalCollocationDensityGrid(params, orbitals, webgl) {
         return { grid, isovalues };
     });
 }
-exports.createSphericalCollocationDensityGrid = createSphericalCollocationDensityGrid;
 function computeDensityIsocontourValues(input, cumulativeThreshold) {
     let weightSum = 0;
     for (let i = 0, _i = input.length; i < _i; i++) {
@@ -106,4 +106,3 @@ function computeDensityIsocontourValues(input, cumulativeThreshold) {
         positive: positive !== Number.POSITIVE_INFINITY ? positive : void 0,
     };
 }
-exports.computeDensityIsocontourValues = computeDensityIsocontourValues;