molstar 3.3.0 → 3.5.0

package/lib/commonjs/servers/model/config.js

@@ -7,10 +7,10 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.configureServer = exports.ModelServerConfigTemplate = exports.ModelServerConfig = exports.mapSourceAndIdToFilename = exports.ModelServerFetchFormats = void 0;
 var tslib_1 = require("tslib");
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
+var argparse = tslib_1.__importStar(require("argparse"));
 var type_helpers_1 = require("../../mol-util/type-helpers");
 var version_1 = require("./version");
-var fs = (0, tslib_1.__importStar)(require("fs"));
+var fs = tslib_1.__importStar(require("fs"));
 var DefaultModelServerConfig = {
     // 0 for off
     cacheMaxSizeInBytes: 2 * 1014 * 1024 * 1024,
@@ -185,8 +185,8 @@ function addServerArgs(parser) {
         ].join('\n'),
     });
 }
-exports.ModelServerConfig = (0, tslib_1.__assign)({}, DefaultModelServerConfig);
-exports.ModelServerConfigTemplate = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultModelServerConfig), { defaultSource: 'pdb-bcif', sourceMap: [
+exports.ModelServerConfig = tslib_1.__assign({}, DefaultModelServerConfig);
+exports.ModelServerConfigTemplate = tslib_1.__assign(tslib_1.__assign({}, DefaultModelServerConfig), { defaultSource: 'pdb-bcif', sourceMap: [
         ['pdb-bcif', './path-to-binary-cif/${id.substr(1, 2)}/${id}.bcif'],
         ['pdb-cif', './path-to-text-cif/${id.substr(1, 2)}/${id}.cif'],
         ['pdb-updated', 'https://www.ebi.ac.uk/pdbe/entry-files/download/${id}_updated.cif', 'cif']
@@ -222,7 +222,7 @@ function validateConfigAndSetupSourceMap() {
     if (!exports.ModelServerConfig.sourceMap || exports.ModelServerConfig.sourceMap.length === 0) {
         throw new Error("Please provide 'sourceMap' configuration. See [-h] for available options.");
     }
-    exports.mapSourceAndIdToFilename = new Function('source', 'id', (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([
+    exports.mapSourceAndIdToFilename = new Function('source', 'id', tslib_1.__spreadArray(tslib_1.__spreadArray([
         'switch (source.toLowerCase()) {'
     ], exports.ModelServerConfig.sourceMap.map(function (_a) {
         var source = _a[0], path = _a[1], format = _a[2];

package/lib/commonjs/servers/model/preprocess/converter.js

@@ -31,9 +31,9 @@ function classify(name, field) {
 }
 function classifyCif(frame) {
     var _this = this;
-    return mol_task_1.Task.create('Classify CIF Data', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Classify CIF Data', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var maxProgress, _i, _a, c, ret, current, _b, _c, c, cat, fields, _d, _e, f, cifField;
-        return (0, tslib_1.__generator)(this, function (_f) {
+        return tslib_1.__generator(this, function (_f) {
             switch (_f.label) {
                 case 0:
                     maxProgress = 0;

package/lib/commonjs/servers/model/preprocess/master.js

@@ -6,9 +6,9 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
+var fs = tslib_1.__importStar(require("fs"));
+var path = tslib_1.__importStar(require("path"));
+var argparse = tslib_1.__importStar(require("argparse"));
 var parallel_1 = require("./parallel");
 function description() {
     var exampleCfg = {

package/lib/commonjs/servers/model/preprocess/parallel.js

@@ -7,8 +7,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.runChild = exports.runMaster = void 0;
 var tslib_1 = require("tslib");
-var path = (0, tslib_1.__importStar)(require("path"));
-var cluster_1 = (0, tslib_1.__importDefault)(require("cluster"));
+var path = tslib_1.__importStar(require("path"));
+var cluster_1 = tslib_1.__importDefault(require("cluster"));
 var now_1 = require("../../../mol-util/now");
 var performance_monitor_1 = require("../../../mol-util/performance-monitor");
 var preprocess_1 = require("./preprocess");
@@ -47,9 +47,9 @@ function runChild() {
     var _this = this;
     process.on('message', function (_a) {
         var entries = _a.entries, config = _a.config;
-        return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var props, _i, entries_1, entry, e_1;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         props = (0, property_provider_1.createModelPropertiesProvider)(config.customProperties);
@@ -85,9 +85,9 @@ function runChild() {
 }
 exports.runChild = runChild;
 function runSingle(entry, config, onMessage) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var props, e_2;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     props = (0, property_provider_1.createModelPropertiesProvider)(config.customProperties);

package/lib/commonjs/servers/model/preprocess/preprocess.js

@@ -20,9 +20,9 @@ function preprocessFile(filename, propertyProvider, outputCif, outputBcif) {
 }
 exports.preprocessFile = preprocessFile;
 function preprocess(filename, propertyProvider, outputCif, outputBcif) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var input, categories, inputStructures, exportCtx, writer, encoder, writer, encoder;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, (0, structure_wrapper_1.readStructureWrapper)('entry', '_local_', filename, void 0, propertyProvider)];
                 case 1:
@@ -52,9 +52,9 @@ function preprocess(filename, propertyProvider, outputCif, outputBcif) {
     });
 }
 function convert(filename, outputCif, outputBcif) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var frame, categories, writer, encoder, writer, encoder;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, (0, structure_wrapper_1.readDataAndFrame)(filename)];
                 case 1:

package/lib/commonjs/servers/model/preprocess.js

@@ -7,7 +7,7 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var cluster_1 = (0, tslib_1.__importDefault)(require("cluster"));
+var cluster_1 = tslib_1.__importDefault(require("cluster"));
 var parallel_1 = require("./preprocess/parallel");
 if (cluster_1.default.isPrimary) {
     require('./preprocess/master');

package/lib/commonjs/servers/model/properties/providers/pdbe.js

@@ -7,8 +7,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PDBe_structRefDomain = exports.PDBe_preferredAssembly = exports.PDBe_structureQualityReport = void 0;
 var tslib_1 = require("tslib");
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var path = (0, tslib_1.__importStar)(require("path"));
+var fs = tslib_1.__importStar(require("fs"));
+var path = tslib_1.__importStar(require("path"));
 var prop_1 = require("../../../../extensions/pdbe/structure-quality-report/prop");
 var fetch_retry_1 = require("../../utils/fetch-retry");
 var mol_util_1 = require("../../../../mol-util");
@@ -18,9 +18,9 @@ var console_logger_1 = require("../../../../mol-util/console-logger");
 var util_1 = require("../../../common/util");
 var PDBe_structureQualityReport = function (_a) {
     var model = _a.model, params = _a.params, cache = _a.cache;
-    return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var PDBe_apiSourceJson, data, _b, _c, _d;
-        return (0, tslib_1.__generator)(this, function (_e) {
+        return tslib_1.__generator(this, function (_e) {
             switch (_e.label) {
                 case 0:
                     PDBe_apiSourceJson = useFileSource(params)
@@ -56,9 +56,9 @@ var residuewise_outlier_summary;
         var _this = this;
         // This is for "testing" purposes and should probably only read
         // a single file with the appropriate prop in the "production" version.
-        return function (model) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return function (model) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var key, fn;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 key = "".concat(model.entryId[1]).concat(model.entryId[2]);
                 if (!json.has(key)) {
                     fn = path.join(pathPrefix, "".concat(key, ".json"));
@@ -94,9 +94,9 @@ function useFileSource(params) {
 function apiQueryProvider(urlPrefix, cache) {
     var _this = this;
     var cacheKey = mol_util_1.UUID.create22();
-    return function (model) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return function (model) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var rawData, json, e_1;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     _a.trys.push([0, 3, , 4]);

package/lib/commonjs/servers/model/properties/providers/wwpdb.js

@@ -7,8 +7,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.wwPDB_chemCompAtom = exports.wwPDB_chemCompBond = void 0;
 var tslib_1 = require("tslib");
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var util = (0, tslib_1.__importStar)(require("util"));
+var fs = tslib_1.__importStar(require("fs"));
+var util = tslib_1.__importStar(require("util"));
 var cif_1 = require("../../../../mol-io/reader/cif");
 var util_1 = require("../../../common/util");
 var mmcif_1 = require("../../../../mol-io/reader/cif/schema/mmcif");
@@ -19,9 +19,9 @@ require('util.promisify').shim();
 var readFile = util.promisify(fs.readFile);
 var wwPDB_chemCompBond = function (_a) {
     var model = _a.model, params = _a.params;
-    return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var table, data, entries;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, getChemCompBondTable(getBondTablePath(params))];
                 case 1:
@@ -35,9 +35,9 @@ var wwPDB_chemCompBond = function (_a) {
 };
 exports.wwPDB_chemCompBond = wwPDB_chemCompBond;
 function read(path) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _a, _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     if (!path.endsWith('.bcif')) return [3 /*break*/, 2];
@@ -56,9 +56,9 @@ function read(path) {
 }
 var chemCompBondTable;
 function getChemCompBondTable(path) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var parsed, _a, _b, table;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     if (!!chemCompBondTable) return [3 /*break*/, 3];
@@ -85,9 +85,9 @@ function getBondTablePath(params) {
 }
 var wwPDB_chemCompAtom = function (_a) {
     var model = _a.model, params = _a.params;
-    return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var table, data, entries;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, getChemCompAtomTable(getAtomTablePath(params))];
                 case 1:
@@ -102,9 +102,9 @@ var wwPDB_chemCompAtom = function (_a) {
 exports.wwPDB_chemCompAtom = wwPDB_chemCompAtom;
 var chemCompAtomTable;
 function getChemCompAtomTable(path) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var parsed, _a, _b, table;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     if (!!chemCompAtomTable) return [3 /*break*/, 3];

package/lib/commonjs/servers/model/property-provider.js

@@ -7,12 +7,12 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.createModelPropertiesProvider = exports.createModelPropertiesProviderFromConfig = void 0;
 var tslib_1 = require("tslib");
-var fs = (0, tslib_1.__importStar)(require("fs"));
+var fs = tslib_1.__importStar(require("fs"));
 var config_1 = require("./config");
 var console_logger_1 = require("../../mol-util/console-logger");
 // TODO enable dynamic imports again
-var pdbeProps = (0, tslib_1.__importStar)(require("./properties/pdbe"));
-var wwpdbProps = (0, tslib_1.__importStar)(require("./properties/wwpdb"));
+var pdbeProps = tslib_1.__importStar(require("./properties/pdbe"));
+var wwpdbProps = tslib_1.__importStar(require("./properties/wwpdb"));
 var attachModelProperties = {
     pdbe: pdbeProps.attachModelProperties,
     wwpdb: wwpdbProps.attachModelProperties

package/lib/commonjs/servers/model/query.js

@@ -7,7 +7,7 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var fs = (0, tslib_1.__importStar)(require("fs"));
+var fs = tslib_1.__importStar(require("fs"));
 var version_1 = require("./version");
 var api_local_1 = require("./server/api-local");
 console.log("Mol* ModelServer (".concat(version_1.VERSION, "), (c) 2018-2020 Mol* authors"));

package/lib/commonjs/servers/model/server/api-local.js

@@ -16,9 +16,9 @@ var jobs_1 = require("./jobs");
 var query_1 = require("./query");
 var structure_wrapper_1 = require("./structure-wrapper");
 function runLocal(input) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _i, input_1, job_1, binary, started, job, key, progress, e_1;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     if (!input.length) {

package/lib/commonjs/servers/model/server/api-schema.js

@@ -121,7 +121,7 @@ function getQueryInfo(def) {
             tags: ['General'],
             summary: def.description,
             operationId: def.name,
-            parameters: (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([
+            parameters: tslib_1.__spreadArray(tslib_1.__spreadArray([
                 { $ref: '#/components/parameters/id' }
             ], def.restParams.map(getParamInfo), true), api_1.CommonQueryParamsInfo.map(getParamInfo), true),
             responses: {
@@ -138,7 +138,7 @@ function getQueryInfo(def) {
             tags: ['General'],
             summary: def.description,
             operationId: def.name + '-post',
-            parameters: (0, tslib_1.__spreadArray)([
+            parameters: tslib_1.__spreadArray([
                 { $ref: '#/components/parameters/id' }
             ], api_1.CommonQueryParamsInfo.map(getParamInfo), true),
             requestBody: {

package/lib/commonjs/servers/model/server/api-web.js

@@ -7,9 +7,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.initWebApi = exports.createResultWriter = void 0;
 var tslib_1 = require("tslib");
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var bodyParser = (0, tslib_1.__importStar)(require("body-parser"));
+var fs = tslib_1.__importStar(require("fs"));
+var path = tslib_1.__importStar(require("path"));
+var bodyParser = tslib_1.__importStar(require("body-parser"));
 var config_1 = require("../config");
 var console_logger_1 = require("../../../mol-util/console-logger");
 var query_1 = require("./query");
@@ -25,9 +25,9 @@ function makePath(p) {
 }
 var responseMap = new Map();
 function processNextJob() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var job, writer, e_1;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     if (!jobs_1.JobManager.hasNext())

package/lib/commonjs/servers/model/server/api.js

@@ -90,7 +90,7 @@ var QueryMap = {
         description: 'Coordinates of the first group satisfying the given criteria.',
         query: function (p, _s, numModels) {
             var tests = (0, atoms_1.getAtomsTests)(p.atom_site);
-            var ligands = structure_1.Queries.combinators.merge(tests.map(function (test) { return structure_1.Queries.generators.atoms((0, tslib_1.__assign)((0, tslib_1.__assign)({}, test), { unitTest: function (ctx) { return structure_1.StructureProperties.unit.model_num(ctx.element) === numModels[0]; }, groupBy: function (ctx) { return structure_1.StructureProperties.residue.key(ctx.element); } })); }));
+            var ligands = structure_1.Queries.combinators.merge(tests.map(function (test) { return structure_1.Queries.generators.atoms(tslib_1.__assign(tslib_1.__assign({}, test), { unitTest: function (ctx) { return structure_1.StructureProperties.unit.model_num(ctx.element) === numModels[0]; }, groupBy: function (ctx) { return structure_1.StructureProperties.residue.key(ctx.element); } })); }));
             return structure_1.Queries.filters.first(ligands);
         },
         jsonParams: [AtomSiteTestJsonParam],
@@ -136,7 +136,7 @@ var QueryMap = {
         description: 'Identifies all residues within the given radius from the source residue. Takes crystal symmetry into account.',
         query: function (p) {
             var tests = (0, atoms_1.getAtomsTests)(p.atom_site);
-            var center = structure_1.Queries.combinators.merge(tests.map(function (test) { return structure_1.Queries.generators.atoms((0, tslib_1.__assign)((0, tslib_1.__assign)({}, test), { entityTest: test.entityTest
+            var center = structure_1.Queries.combinators.merge(tests.map(function (test) { return structure_1.Queries.generators.atoms(tslib_1.__assign(tslib_1.__assign({}, test), { entityTest: test.entityTest
                     ? function (ctx) { return test.entityTest(ctx) && ctx.element.unit.conformation.operator.isIdentity; }
                     : function (ctx) { return ctx.element.unit.conformation.operator.isIdentity; } })); }));
             return structure_1.Queries.modifiers.includeSurroundings(center, { radius: p.radius !== void 0 ? p.radius : 5, wholeResidues: true });
@@ -147,7 +147,7 @@ var QueryMap = {
             return structure_1.StructureSymmetry.builderSymmetryMates(s, p.radius !== void 0 ? p.radius : 5).run();
         },
         jsonParams: [AtomSiteTestJsonParam, RadiusParam, AssemblyNameParam],
-        restParams: (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], exports.AtomSiteTestRestParams, true), [RadiusParam, AssemblyNameParam], false),
+        restParams: tslib_1.__spreadArray(tslib_1.__spreadArray([], exports.AtomSiteTestRestParams, true), [RadiusParam, AssemblyNameParam], false),
         filter: schemas_1.QuerySchemas.interaction
     }),
     'residueSurroundings': Q({
@@ -158,7 +158,7 @@ var QueryMap = {
             return structure_1.Queries.modifiers.includeSurroundings(center, { radius: p.radius, wholeResidues: true });
         },
         jsonParams: [AtomSiteTestJsonParam, RadiusParam],
-        restParams: (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], exports.AtomSiteTestRestParams, true), [RadiusParam], false),
+        restParams: tslib_1.__spreadArray(tslib_1.__spreadArray([], exports.AtomSiteTestRestParams, true), [RadiusParam], false),
         filter: schemas_1.QuerySchemas.interaction
     }),
     'surroundingLigands': Q({
@@ -166,7 +166,7 @@ var QueryMap = {
         description: 'Identifies (complete) ligands within the given radius from the source atom set. Takes crystal symmetry into account.',
         query: function (p) {
             var tests = (0, atoms_1.getAtomsTests)(p.atom_site);
-            var center = structure_1.Queries.combinators.merge(tests.map(function (test) { return structure_1.Queries.generators.atoms((0, tslib_1.__assign)((0, tslib_1.__assign)({}, test), { entityTest: test.entityTest
+            var center = structure_1.Queries.combinators.merge(tests.map(function (test) { return structure_1.Queries.generators.atoms(tslib_1.__assign(tslib_1.__assign({}, test), { entityTest: test.entityTest
                     ? function (ctx) { return test.entityTest(ctx) && ctx.element.unit.conformation.operator.isIdentity; }
                     : function (ctx) { return ctx.element.unit.conformation.operator.isIdentity; } })); }));
             return structure_1.Queries.modifiers.surroundingLigands({ query: center, radius: p.radius !== void 0 ? p.radius : 5, includeWater: !p.omit_water });
@@ -177,7 +177,7 @@ var QueryMap = {
             return structure_1.StructureSymmetry.builderSymmetryMates(s, p.radius !== void 0 ? p.radius : 5).run();
         },
         jsonParams: [AtomSiteTestJsonParam, RadiusParam, OmitWaterParam, AssemblyNameParam],
-        restParams: (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], exports.AtomSiteTestRestParams, true), [RadiusParam, OmitWaterParam, AssemblyNameParam], false),
+        restParams: tslib_1.__spreadArray(tslib_1.__spreadArray([], exports.AtomSiteTestRestParams, true), [RadiusParam, OmitWaterParam, AssemblyNameParam], false),
         filter: schemas_1.QuerySchemas.interaction
     }),
 };

package/lib/commonjs/servers/model/server/query.js

@@ -7,7 +7,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.abortingObserver = exports.resolveJob = void 0;
 var tslib_1 = require("tslib");
-var path = (0, tslib_1.__importStar)(require("path"));
+var path = tslib_1.__importStar(require("path"));
 var cif_1 = require("../../../mol-io/writer/cif");
 var structure_1 = require("../../../mol-model/structure");
 var mmcif_1 = require("../../../mol-model/structure/export/mmcif");
@@ -38,8 +38,8 @@ function propertyProvider() {
     return _propertyProvider;
 }
 function resolveJob(job) {
-    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) {
             if (job.responseFormat.tarball) {
                 return [2 /*return*/, resolveMultiFile(job)];
             }
@@ -54,22 +54,22 @@ exports.resolveJob = resolveJob;
 var SharedParams = {
     encoderName: "ModelServer ".concat(version_1.VERSION)
 };
-var SharedLigandWritingParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, SharedParams), { hydrogens: true });
+var SharedLigandWritingParams = tslib_1.__assign(tslib_1.__assign({}, SharedParams), { hydrogens: true });
 function createEncoder(job) {
     switch (job.responseFormat.encoding) {
         case 'bcif':
-            return cif_1.CifWriter.createEncoder((0, tslib_1.__assign)((0, tslib_1.__assign)({}, SharedParams), { binary: true, binaryAutoClassifyEncoding: true }));
+            return cif_1.CifWriter.createEncoder(tslib_1.__assign(tslib_1.__assign({}, SharedParams), { binary: true, binaryAutoClassifyEncoding: true }));
         case 'sdf':
             ensureCompatibleQueryType(job);
-            return sdf_1.SdfWriter.createEncoder((0, tslib_1.__assign)({}, SharedLigandWritingParams));
+            return sdf_1.SdfWriter.createEncoder(tslib_1.__assign({}, SharedLigandWritingParams));
         case 'mol':
             ensureCompatibleQueryType(job);
-            return mol_1.MolWriter.createEncoder((0, tslib_1.__assign)({}, SharedLigandWritingParams));
+            return mol_1.MolWriter.createEncoder(tslib_1.__assign({}, SharedLigandWritingParams));
         case 'mol2':
             ensureCompatibleQueryType(job);
-            return mol2_1.Mol2Writer.createEncoder((0, tslib_1.__assign)({}, SharedLigandWritingParams));
+            return mol2_1.Mol2Writer.createEncoder(tslib_1.__assign({}, SharedLigandWritingParams));
         default:
-            return cif_1.CifWriter.createEncoder((0, tslib_1.__assign)((0, tslib_1.__assign)({}, SharedParams), { binary: false, binaryAutoClassifyEncoding: true }));
+            return cif_1.CifWriter.createEncoder(tslib_1.__assign(tslib_1.__assign({}, SharedParams), { binary: false, binaryAutoClassifyEncoding: true }));
     }
 }
 function ensureCompatibleQueryType(job) {
@@ -80,9 +80,9 @@ function ensureCompatibleQueryType(job) {
     });
 }
 function resolveSingleFile(job) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var encoder, headerMap, _i, _a, entry, hasDataBlock, structure, header, i, e_1;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     console_logger_1.ConsoleLogger.logId(job.id, 'Query', "Starting (format: ".concat(job.responseFormat.encoding, ")."));
@@ -144,9 +144,9 @@ function getFilename(i, entry, header, encoding) {
     return "".concat(i, "_").concat(header.toLowerCase(), "_").concat((0, string_1.splitCamelCase)(entry.queryDefinition.name.replace(/\s/g, '_'), '-').toLowerCase(), ".").concat(encoding);
 }
 function resolveMultiFile(job) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var i, _i, _a, entry, encoder, hasDataBlock, header, structure, e_2;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     console_logger_1.ConsoleLogger.logId(job.id, 'Query', 'Starting.');
@@ -206,9 +206,9 @@ function createErrorDataBlock(job, encoder) {
     return header;
 }
 function resolveJobEntry(entry, structure, encoder) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var sourceStructures, structures, _i, sourceStructures_1, s, _a, _b, modelNums_1, queries, result, i, s, stats, e_3;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     console_logger_1.ConsoleLogger.logId(entry.job.id, 'Query', "Start ".concat(entry.key, "/").concat(entry.queryDefinition.name, "."));

package/lib/commonjs/servers/model/server/structure-wrapper.js

@@ -12,9 +12,9 @@ var performance_monitor_1 = require("../../../mol-util/performance-monitor");
 var cache_1 = require("./cache");
 var config_1 = require("../config");
 var cif_1 = require("../../../mol-io/reader/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 console_logger_1 = require("../../../mol-util/console-logger");
 var mmcif_1 = require("../../../mol-model-formats/structure/mmcif");
 var fetch_retry_1 = require("../utils/fetch-retry");
@@ -27,9 +27,9 @@ var StructureSourceType;
 })(StructureSourceType = exports.StructureSourceType || (exports.StructureSourceType = {}));
 function createStructureWrapperFromJobEntry(entry, propertyProvider, allowCache) {
     if (allowCache === void 0) { allowCache = true; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ret_1, ret;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     if (allowCache && config_1.ModelServerConfig.cacheMaxSizeInBytes > 0) {
@@ -54,10 +54,10 @@ var perf = new performance_monitor_1.PerformanceMonitor();
 var readFileAsync = util.promisify(fs.readFile);
 var unzipAsync = util.promisify(zlib.unzip);
 function readFile(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, data, i, data, _a;
         var _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     isGz = /\.gz$/i.test(filename);
@@ -92,9 +92,9 @@ function readFile(filename) {
     });
 }
 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);
@@ -109,9 +109,9 @@ function parseCif(data) {
     });
 }
 function readDataAndFrame(filename, key) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var data, isBinary, read, e_1, frame;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     perf.start('read');
@@ -142,9 +142,9 @@ function readDataAndFrame(filename, key) {
 }
 exports.readDataAndFrame = readDataAndFrame;
 function fetchDataAndFrame(jobId, uri, format, key) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var isBinary, data, response, input, _a, i, _b, _c, e_2, frame;
-        return (0, tslib_1.__generator)(this, function (_d) {
+        return tslib_1.__generator(this, function (_d) {
             switch (_d.label) {
                 case 0:
                     perf.start('read');
@@ -215,9 +215,9 @@ function readOrFetch(jobId, key, sourceId, entryId) {
     return readDataAndFrame(mapped[0], key);
 }
 function readStructureWrapper(key, sourceId, entryId, jobId, propertyProvider) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _a, data, frame, isBinary, trajectory, models, modelMap, i, m, ret;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, readOrFetch(jobId || '', key, sourceId, entryId)];
                 case 1:
@@ -270,9 +270,9 @@ function readStructureWrapper(key, sourceId, entryId, jobId, propertyProvider) {
 }
 exports.readStructureWrapper = readStructureWrapper;
 function resolveStructure(wrapper, modelNum) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var model, structure, modelProps, _i, modelProps_1, p;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     if (typeof modelNum === 'undefined')
@@ -305,9 +305,9 @@ function resolveStructure(wrapper, modelNum) {
 }
 exports.resolveStructure = resolveStructure;
 function resolveStructures(wrapper, modelNums) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ret, _i, _a, n, s;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     ret = [];
@@ -332,9 +332,9 @@ function resolveStructures(wrapper, modelNums) {
 }
 exports.resolveStructures = resolveStructures;
 function tryAttach(key, promise) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var e_3;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     _a.trys.push([0, 2, , 3]);

package/lib/commonjs/servers/model/server.js

@@ -7,8 +7,8 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var compression_1 = (0, tslib_1.__importDefault)(require("compression"));
-var express_1 = (0, tslib_1.__importDefault)(require("express"));
+var compression_1 = tslib_1.__importDefault(require("compression"));
+var express_1 = tslib_1.__importDefault(require("express"));
 var console_logger_1 = require("../../mol-util/console-logger");
 var performance_monitor_1 = require("../../mol-util/performance-monitor");
 var config_1 = require("./config");

package/lib/commonjs/servers/model/utils/fetch-props-pdbe.js

@@ -6,10 +6,10 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
+var node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
+var fs = tslib_1.__importStar(require("fs"));
+var path = tslib_1.__importStar(require("path"));
+var argparse = tslib_1.__importStar(require("argparse"));
 var make_dir_1 = require("../../../mol-util/make-dir");
 var now_1 = require("../../../mol-util/now");
 var performance_monitor_1 = require("../../../mol-util/performance-monitor");
@@ -52,9 +52,9 @@ function findEntries() {
     return ret;
 }
 function process() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var entries, started, prog, _i, entries_1, e, ts, data, _a, _b, ee, query, _c, _d, e_1, time;
-        return (0, tslib_1.__generator)(this, function (_e) {
+        return tslib_1.__generator(this, function (_e) {
             switch (_e.label) {
                 case 0:
                     entries = findEntries();