molstar 4.3.0 → 4.4.0

package/lib/commonjs/apps/viewer/app.d.ts

@@ -3,10 +3,12 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Neli Fonseca <neli@ebi.ac.uk>
  */
 import { loadMVS } from '../../extensions/mvs/load';
 import { MVSData } from '../../extensions/mvs/mvs-data';
 import { SaccharideCompIdMapType } from '../../mol-model/structure/structure/carbohydrates/constants';
+import { Volume } from '../../mol-model/volume';
 import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
 import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
@@ -44,7 +46,7 @@ export declare const ExtensionMap: {
     tunnels: PluginSpec.Behavior;
 };
 declare const DefaultViewerOptions: {
-    customFormats: [string, DataFormatProvider<any, any, any>][];
+    customFormats: [string, DataFormatProvider][];
     extensions: ("mp4-export" | "backgrounds" | "dnatco-ntcs" | "g3d" | "geo-export" | "model-export" | "mvs" | "pdbe-structure-quality-report" | "sb-ncbr-partial-charges" | "volseg" | "wwpdb-chemical-component-dictionary" | "zenodo-import" | "assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment" | "tunnels")[];
     disabledExtensions: string[];
     layoutIsExpanded: boolean;
@@ -148,6 +150,10 @@ export declare class Viewer {
         entryId?: string | string[];
         isLazy?: boolean;
     }): Promise<void>;
+    loadFullResolutionEMDBMap(emdbId: string, options: {
+        isoValue: Volume.IsoValue;
+        color?: Color;
+    }): Promise<void>;
     /**
      * @example
      *  viewer.loadTrajectory({
@@ -290,12 +296,12 @@ export declare const PluginExtensions: {
         MVSData: {
             SupportedVersion: number;
             fromMVSJ(mvsjString: string): MVSData;
-            toMVSJ(mvsData: MVSData, space?: string | number | undefined): string;
+            toMVSJ(mvsData: MVSData, space?: string | number): string;
             isValid(mvsData: MVSData, options?: {
-                noExtra?: boolean | undefined;
+                noExtra?: boolean;
             }): boolean;
             validationIssues(mvsData: MVSData, options?: {
-                noExtra?: boolean | undefined;
+                noExtra?: boolean;
             }): string[] | undefined;
             toPrettyString(mvsData: MVSData): string;
             createBuilder(): import("../../extensions/mvs/tree/mvs/mvs-builder").Root;

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");
@@ -393,6 +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/create-ions.js

@@ -28,15 +28,15 @@ function extractIonNames(ccd) {
     return ionNames;
 }
 function writeIonNamesFile(filePath, ionNames) {
-    const output = `/**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated ion names params file. Names extracted from CCD components.
- *
- * @author molstar/chem-comp-dict/create-ions cli
- */
-
-export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
+    const output = `/**
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/chem-comp-dict/create-ions cli
+ */
+
+export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
 `;
     writeFile(filePath, output);
 }

package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js

@@ -29,15 +29,15 @@ function extractSaccharideNames(ccd) {
     return saccharideNames;
 }
 function writeSaccharideNamesFile(filePath, ionNames) {
-    const output = `/**
- * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated ion names params file. Names extracted from CCD components.
- *
- * @author molstar/cli/chem-comp-dict/create-saccharides
- */
-
-export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
+    const output = `/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/cli/chem-comp-dict/create-saccharides
+ */
+
+export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
 `;
     writeFile(filePath, output);
 }

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

@@ -5,25 +5,25 @@
  * @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) {
-    return `/**
- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated '${name}' schema file. ${info}
- *
- * @author molstar/ciftools package
- */
-
-import { Database, Column } from '${moldataImportPath}/db';
-
+    return `/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated '${name}' schema file. ${info}
+ *
+ * @author molstar/ciftools package
+ */
+
+import { Database, Column } from '${moldataImportPath}/db';
+
 import Schema = Column.Schema;`;
 }
 function footer(name) {
-    return `
-export type ${name}_Schema = typeof ${name}_Schema;
+    return `
+export type ${name}_Schema = typeof ${name}_Schema;
 export interface ${name}_Database extends Database<${name}_Schema> {};`;
 }
 function getTypeShorthands(schema, fields) {
@@ -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/lipid-params/index.js

@@ -44,15 +44,15 @@ async function run(out) {
     }
     const lipidNames = JSON.stringify(lipids.array);
     if (out) {
-        const output = `/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
- *
- * @author molstar/lipid-params cli
- */
-
-export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
+        const output = `/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
+ *
+ * @author molstar/lipid-params cli
+ */
+
+export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
 `;
         fs.writeFileSync(out, output);
     }

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);