molstar 3.3.1 → 3.4.0

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

@@ -20,6 +20,7 @@ var model_export_1 = require("../../extensions/model-export");
 var mp4_export_1 = require("../../extensions/mp4-export");
 var pdbe_1 = require("../../extensions/pdbe");
 var rcsb_1 = require("../../extensions/rcsb");
+var zenodo_1 = require("../../extensions/zenodo");
 var volume_1 = require("../../mol-model/volume");
 var structure_1 = require("../../mol-plugin-state/actions/structure");
 var volume_2 = require("../../mol-plugin-state/actions/volume");
@@ -56,6 +57,7 @@ var Extensions = {
     'mp4-export': spec_2.PluginSpec.Behavior(mp4_export_1.Mp4Export),
     'geo-export': spec_2.PluginSpec.Behavior(geo_export_1.GeometryExport),
     'ma-quality-assessment': spec_2.PluginSpec.Behavior(behavior_2.MAQualityAssessment),
+    'zenodo-import': spec_2.PluginSpec.Behavior(zenodo_1.ZenodoImport),
 };
 var DefaultViewerOptions = {
     customFormats: CustomFormats,
@@ -93,9 +95,9 @@ var Viewer = /** @class */ (function () {
     Viewer.create = function (elementOrId, options) {
         var _a;
         if (options === void 0) { options = {}; }
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var definedOptions, _i, _b, p, o, defaultSpec, spec, element, plugin;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
                         definedOptions = {};
@@ -106,12 +108,12 @@ var Viewer = /** @class */ (function () {
                             if (options[p] !== void 0)
                                 definedOptions[p] = options[p];
                         }
-                        o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), definedOptions);
+                        o = tslib_1.__assign(tslib_1.__assign({}, DefaultViewerOptions), definedOptions);
                         defaultSpec = (0, spec_1.DefaultPluginUISpec)();
                         spec = {
                             actions: defaultSpec.actions,
-                            behaviors: (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], defaultSpec.behaviors, true), o.extensions.map(function (e) { return Extensions[e]; }), true),
-                            animations: (0, tslib_1.__spreadArray)([], defaultSpec.animations || [], true),
+                            behaviors: tslib_1.__spreadArray(tslib_1.__spreadArray([], defaultSpec.behaviors, true), o.extensions.map(function (e) { return Extensions[e]; }), true),
+                            animations: tslib_1.__spreadArray([], defaultSpec.animations || [], true),
                             customParamEditors: defaultSpec.customParamEditors,
                             customFormats: o === null || o === void 0 ? void 0 : o.customFormats,
                             layout: {
@@ -127,7 +129,7 @@ var Viewer = /** @class */ (function () {
                                     }
                                 },
                             },
-                            components: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, defaultSpec.components), { controls: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (_a = defaultSpec.components) === null || _a === void 0 ? void 0 : _a.controls), { top: o.layoutShowSequence ? undefined : 'none', bottom: o.layoutShowLog ? undefined : 'none', left: o.layoutShowLeftPanel ? undefined : 'none' }), remoteState: o.layoutShowRemoteState ? 'default' : 'none' }),
+                            components: tslib_1.__assign(tslib_1.__assign({}, defaultSpec.components), { controls: tslib_1.__assign(tslib_1.__assign({}, (_a = defaultSpec.components) === null || _a === void 0 ? void 0 : _a.controls), { top: o.layoutShowSequence ? undefined : 'none', bottom: o.layoutShowLog ? undefined : 'none', left: o.layoutShowLeftPanel ? undefined : 'none' }), remoteState: o.layoutShowRemoteState ? 'default' : 'none' }),
                             config: [
                                 [config_1.PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
                                 [config_1.PluginConfig.General.PixelScale, o.pixelScale],
@@ -186,7 +188,7 @@ var Viewer = /** @class */ (function () {
                     url: assets_1.Asset.Url(url),
                     format: format,
                     isBinary: isBinary,
-                    options: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
+                    options: tslib_1.__assign(tslib_1.__assign({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
                 }
             }
         }));
@@ -194,9 +196,9 @@ var Viewer = /** @class */ (function () {
     Viewer.prototype.loadAllModelsOrAssemblyFromUrl = function (url, format, isBinary, options) {
         if (format === void 0) { format = 'mmcif'; }
         if (isBinary === void 0) { isBinary = false; }
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var plugin, data, trajectory;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         plugin = this.plugin;
@@ -215,9 +217,9 @@ var Viewer = /** @class */ (function () {
         });
     };
     Viewer.prototype.loadStructureFromData = function (data, format, options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var _data, trajectory;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, this.plugin.builders.data.rawData({ data: data, label: options === null || options === void 0 ? void 0 : options.dataLabel })];
                     case 1:
@@ -247,7 +249,7 @@ var Viewer = /** @class */ (function () {
                             params: structure_1.PdbDownloadProvider[provider].defaultValue
                         }
                     },
-                    options: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
+                    options: tslib_1.__assign(tslib_1.__assign({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
                 }
             }
         }));
@@ -290,7 +292,7 @@ var Viewer = /** @class */ (function () {
                 name: 'alphafolddb',
                 params: {
                     id: afdb,
-                    options: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.source.params.options), { representation: 'preset-structure-representation-ma-quality-assessment-plddt' }),
+                    options: tslib_1.__assign(tslib_1.__assign({}, params.source.params.options), { representation: 'preset-structure-representation-ma-quality-assessment-plddt' }),
                 }
             }
         }));
@@ -348,10 +350,10 @@ var Viewer = /** @class */ (function () {
      */
     Viewer.prototype.loadVolumeFromUrl = function (_a, isovalues, options) {
         var url = _a.url, format = _a.format, isBinary = _a.isBinary;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var plugin, update;
             var _this = this;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 plugin = this.plugin;
                 if (!plugin.dataFormats.get(format)) {
                     throw new Error("Unknown density format: ".concat(format));
@@ -363,14 +365,14 @@ var Viewer = /** @class */ (function () {
                         format: format,
                         entryId: options === null || options === void 0 ? void 0 : options.entryId,
                         isBinary: isBinary,
-                        isovalues: isovalues.map(function (v) { return ((0, tslib_1.__assign)({ alpha: 1, volumeIndex: 0 }, v)); })
+                        isovalues: isovalues.map(function (v) { return (tslib_1.__assign({ alpha: 1, volumeIndex: 0 }, v)); })
                     });
                     return [2 /*return*/, update.commit()];
                 }
-                return [2 /*return*/, plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                return [2 /*return*/, plugin.dataTransaction(function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                         var data, parsed, firstVolume, repr, _i, isovalues_1, iso, volume, volumeData;
                         var _a, _b, _c, _d;
-                        return (0, tslib_1.__generator)(this, function (_e) {
+                        return tslib_1.__generator(this, function (_e) {
                             switch (_e.label) {
                                 case 0: return [4 /*yield*/, plugin.builders.data.download({ url: url, isBinary: isBinary }, { state: { isGhost: true } })];
                                 case 1:
@@ -415,9 +417,9 @@ var Viewer = /** @class */ (function () {
      */
     Viewer.prototype.loadTrajectory = function (params) {
         var _a, _b;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var plugin, model, coords, data, _c, trajectory_1, data, _d, provider, data, _e, provider, trajectory, preset;
-            return (0, tslib_1.__generator)(this, function (_f) {
+            return tslib_1.__generator(this, function (_f) {
                 switch (_f.label) {
                     case 0:
                         plugin = this.plugin;
@@ -508,9 +510,9 @@ exports.ViewerAutoPreset = (0, representation_preset_1.StructureRepresentationPr
     params: function () { return representation_preset_1.StructureRepresentationPresetProvider.CommonParams; },
     apply: function (ref, params, plugin) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, structure;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);

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

@@ -11,4 +11,4 @@ require("./embedded.html");
 require("./favicon.ico");
 require("./index.html");
 require('mol-plugin-ui/skin/light.scss');
-(0, tslib_1.__exportStar)(require("./app"), exports);
+tslib_1.__exportStar(require("./app"), exports);

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

@@ -7,10 +7,10 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var util_1 = (0, tslib_1.__importDefault)(require("util"));
-var fs_1 = (0, tslib_1.__importDefault)(require("fs"));
+var argparse = tslib_1.__importStar(require("argparse"));
+var path = tslib_1.__importStar(require("path"));
+var util_1 = tslib_1.__importDefault(require("util"));
+var fs_1 = tslib_1.__importDefault(require("fs"));
 require('util.promisify').shim();
 var writeFile = util_1.default.promisify(fs_1.default.writeFile);
 var util_2 = require("./util");
@@ -32,9 +32,9 @@ function writeIonNamesFile(filePath, ionNames) {
 }
 function run(out, forceDownload) {
     if (forceDownload === void 0) { forceDownload = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ccd, ionNames;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, (0, util_2.ensureDataAvailable)(forceDownload)];
                 case 1:

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

@@ -0,0 +1,7 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+export {};

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

@@ -0,0 +1,69 @@
+#!/usr/bin/env node
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+var tslib_1 = require("tslib");
+var argparse = tslib_1.__importStar(require("argparse"));
+var path = tslib_1.__importStar(require("path"));
+var util_1 = tslib_1.__importDefault(require("util"));
+var fs_1 = tslib_1.__importDefault(require("fs"));
+require('util.promisify').shim();
+var writeFile = util_1.default.promisify(fs_1.default.writeFile);
+var util_2 = require("./util");
+function extractSaccharideNames(ccd) {
+    var saccharideNames = [];
+    for (var k in ccd) {
+        var chem_comp = ccd[k].chem_comp;
+        var type = chem_comp.type.value(0).toUpperCase();
+        if (type.includes('SACCHARIDE')) {
+            saccharideNames.push(chem_comp.id.value(0));
+        }
+    }
+    // these are extra saccharides that don't have SACCHARIDE in their type
+    saccharideNames.push('UMQ', // UNDECYL-MALTOSIDE, via GlyFinder
+    'SQD');
+    return saccharideNames;
+}
+function writeSaccharideNamesFile(filePath, ionNames) {
+    var output = "/**\n * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated ion names params file. Names extracted from CCD components.\n *\n * @author molstar/cli/chem-comp-dict/create-saccharides\n */\n\nexport const SaccharideNames = new Set(".concat(JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', '), ");\n");
+    writeFile(filePath, output);
+}
+function run(out, forceDownload) {
+    if (forceDownload === void 0) { forceDownload = false; }
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var ccd, saccharideNames;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, (0, util_2.ensureDataAvailable)(forceDownload)];
+                case 1:
+                    _a.sent();
+                    return [4 /*yield*/, (0, util_2.readCCD)()];
+                case 2:
+                    ccd = _a.sent();
+                    saccharideNames = extractSaccharideNames(ccd);
+                    if (!fs_1.default.existsSync(path.dirname(out))) {
+                        fs_1.default.mkdirSync(path.dirname(out));
+                    }
+                    writeSaccharideNamesFile(out, saccharideNames);
+                    return [2 /*return*/];
+            }
+        });
+    });
+}
+var parser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Extract and save SaccharideNames from CCD.'
+});
+parser.add_argument('out', {
+    help: 'Generated file output path.'
+});
+parser.add_argument('--forceDownload', '-f', {
+    action: 'store_true',
+    help: 'Force download of CCD and PVCD.'
+});
+var args = parser.parse_args();
+run(args.out, args.forceDownload);

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

@@ -7,10 +7,10 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
-var util = (0, tslib_1.__importStar)(require("util"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
+var argparse = tslib_1.__importStar(require("argparse"));
+var util = tslib_1.__importStar(require("util"));
+var path = tslib_1.__importStar(require("path"));
+var fs = tslib_1.__importStar(require("fs"));
 require('util.promisify').shim();
 var writeFile = util.promisify(fs.writeFile);
 var db_1 = require("../../mol-data/db");
@@ -103,7 +103,7 @@ function checkAddingAtomsFromPVCD(pvcd) {
     }
 }
 function createBonds(ccd, pvcd, atomsRequested) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         function addBonds(compId, ccb, protonationVariant) {
             for (var i = 0, il = ccb._rowCount; i < il; ++i) {
                 var atomId1 = ccb.atom_id_1.value(i);
@@ -122,7 +122,7 @@ function createBonds(ccd, pvcd, atomsRequested) {
             }
         }
         var ccbSet, comp_id, atom_id_1, atom_id_2, value_order, pdbx_aromatic_flag, pdbx_stereo_config, molstar_protonation_variant, k, _a, chem_comp, chem_comp_bond, parentIds, i, il, k, _b, chem_comp, chem_comp_bond, bondTable, bondDatabase;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             ccbSet = new Set();
             comp_id = [];
             atom_id_1 = [];
@@ -223,9 +223,9 @@ function createAtoms(ccd, pvcd) {
 function run(out, binary, forceDownload, ccaOut) {
     if (binary === void 0) { binary = false; }
     if (forceDownload === void 0) { forceDownload = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ccd, pvcd, _a, bonds, atoms, ccbCif, ccaCif;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, (0, util_1.ensureDataAvailable)(forceDownload)];
                 case 1:

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

@@ -7,11 +7,11 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getEncodedCif = exports.readPVCD = exports.readCCD = exports.readFileAsCollection = exports.ensureDataAvailable = exports.ensureAvailable = void 0;
 var tslib_1 = require("tslib");
-var util = (0, tslib_1.__importStar)(require("util"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var zlib = (0, tslib_1.__importStar)(require("zlib"));
-var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
+var util = tslib_1.__importStar(require("util"));
+var path = tslib_1.__importStar(require("path"));
+var fs = tslib_1.__importStar(require("fs"));
+var zlib = tslib_1.__importStar(require("zlib"));
+var node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
 require('util.promisify').shim();
 var readFile = util.promisify(fs.readFile);
 var writeFile = util.promisify(fs.writeFile);
@@ -21,9 +21,9 @@ var cif_2 = require("../../mol-io/writer/cif");
 var ccd_1 = require("../../mol-io/reader/cif/schema/ccd");
 function ensureAvailable(path, url, forceDownload) {
     if (forceDownload === void 0) { forceDownload = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var data, _a, _b, _c, _d, _e, _f;
-        return (0, tslib_1.__generator)(this, function (_g) {
+        return tslib_1.__generator(this, function (_g) {
             switch (_g.label) {
                 case 0:
                     if (!(forceDownload || !fs.existsSync(path))) return [3 /*break*/, 8];
@@ -62,8 +62,8 @@ function ensureAvailable(path, url, forceDownload) {
 exports.ensureAvailable = ensureAvailable;
 function ensureDataAvailable(forceDownload) {
     if (forceDownload === void 0) { forceDownload = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, ensureAvailable(CCD_PATH, CCD_URL, forceDownload)];
                 case 1:
@@ -78,9 +78,9 @@ function ensureDataAvailable(forceDownload) {
 }
 exports.ensureDataAvailable = ensureDataAvailable;
 function readFileAsCollection(path, schema) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var parsed, _a;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     _a = parseCif;
@@ -95,25 +95,25 @@ function readFileAsCollection(path, schema) {
 }
 exports.readFileAsCollection = readFileAsCollection;
 function readCCD() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, readFileAsCollection(CCD_PATH, ccd_1.CCD_Schema)];
         });
     });
 }
 exports.readCCD = readCCD;
 function readPVCD() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, readFileAsCollection(PVCD_PATH, ccd_1.CCD_Schema)];
         });
     });
 }
 exports.readPVCD = readPVCD;
 function parseCif(data) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var comp, parsed;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     comp = cif_1.CIF.parse(data);

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

@@ -10,9 +10,9 @@ exports.convert = void 0;
 var tslib_1 = require("tslib");
 var cif_1 = require("../../mol-io/reader/cif");
 var cif_2 = require("../../mol-io/writer/cif");
-var util = (0, tslib_1.__importStar)(require("util"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var zlib = (0, tslib_1.__importStar)(require("zlib"));
+var util = tslib_1.__importStar(require("util"));
+var fs = tslib_1.__importStar(require("fs"));
+var zlib = tslib_1.__importStar(require("zlib"));
 var mol_task_1 = require("../../mol-task");
 var binary_cif_1 = require("../../mol-io/common/binary-cif");
 var encoder_1 = require("../../mol-io/writer/cif/encoder");
@@ -23,9 +23,9 @@ function showProgress(p) {
 var readFileAsync = util.promisify(fs.readFile);
 var unzipAsync = util.promisify(zlib.unzip);
 function readFile(ctx, filename) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var isGz, input, str, data, _a;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     isGz = /\.gz$/i.test(filename);
@@ -61,9 +61,9 @@ function readFile(ctx, filename) {
     });
 }
 function getCIF(ctx, filename) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var parsed;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, readFile(ctx, filename)];
                 case 1:
@@ -99,9 +99,9 @@ function classify(name, field) {
 function convert(path, asText, hints, filter) {
     var _this = this;
     if (asText === void 0) { asText = false; }
-    return mol_task_1.Task.create('BinaryCIF', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('BinaryCIF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var encodingProvider, cif, encoder, maxProgress, _i, _a, b, _b, _c, c, current, _d, _e, b, _f, _g, c, cat, fields, _h, _j, f, ret;
-        return (0, tslib_1.__generator)(this, function (_k) {
+        return tslib_1.__generator(this, function (_k) {
             switch (_k.label) {
                 case 0:
                     encodingProvider = hints

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

@@ -8,16 +8,16 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
-var util = (0, tslib_1.__importStar)(require("util"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var zlib = (0, tslib_1.__importStar)(require("zlib"));
+var argparse = tslib_1.__importStar(require("argparse"));
+var util = tslib_1.__importStar(require("util"));
+var fs = tslib_1.__importStar(require("fs"));
+var zlib = tslib_1.__importStar(require("zlib"));
 var converter_1 = require("./converter");
 require('util.promisify').shim();
 function process(srcPath, outPath, configPath, filterPath) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var config, filter, res;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;
@@ -35,9 +35,9 @@ function process(srcPath, outPath, configPath, filterPath) {
 }
 var zipAsync = util.promisify(zlib.gzip);
 function write(outPath, res) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var isGz;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     isGz = /\.gz$/i.test(outPath);