molstar 3.2.0 → 3.4.0

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:
@@ -279,4 +279,3 @@ parser.add_argument('--ccaOut', '-a', {
 });
 var args = parser.parse_args();
 run(args.out, args.binary, args.forceDownload, args.ccaOut);
-//# sourceMappingURL=create-table.js.map

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);
@@ -141,4 +141,3 @@ var CCD_PATH = path.join(DATA_DIR, 'components.cif');
 var PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
 var CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif';
 var PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';
-//# sourceMappingURL=util.js.map

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
@@ -184,4 +184,3 @@ function convert(path, asText, hints, filter) {
     }); }).run(showProgress, 250);
 }
 exports.convert = convert;
-//# sourceMappingURL=converter.js.map

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);
@@ -78,4 +78,3 @@ var args = parser.parse_args();
 if (args) {
     run(args);
 }
-//# sourceMappingURL=index.js.map

package/lib/commonjs/cli/cifschema/index.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 fs = (0, tslib_1.__importStar)(require("fs"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
+var argparse = tslib_1.__importStar(require("argparse"));
+var fs = tslib_1.__importStar(require("fs"));
+var path = tslib_1.__importStar(require("path"));
+var node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
 var parser_1 = require("../../mol-io/reader/csv/parser");
 var parser_2 = require("../../mol-io/reader/cif/text/parser");
 var cif_dic_1 = require("./util/cif-dic");
@@ -24,9 +24,9 @@ function getDicNamespace(block) {
 }
 function runGenerateSchemaMmcif(name, fieldNamesPath, typescript, out, moldbImportPath, addAliases) {
     if (typescript === void 0) { typescript = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var mmcifDic, ihmDic, maDic, mmcifDicVersion, ihmDicVersion, maDicVersion, version, frames, schema;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, ensureMmcifDicAvailable()];
                 case 1:
@@ -56,7 +56,7 @@ function runGenerateSchemaMmcif(name, fieldNamesPath, typescript, out, moldbImpo
                     ihmDicVersion = getDicVersion(ihmDic.result.blocks[0]);
                     maDicVersion = getDicVersion(maDic.result.blocks[0]);
                     version = "Dictionary versions: mmCIF ".concat(mmcifDicVersion, ", IHM ").concat(ihmDicVersion, ", MA ").concat(maDicVersion, ".");
-                    frames = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], mmcifDic.result.blocks[0].saveFrames, true), ihmDic.result.blocks[0].saveFrames, true), maDic.result.blocks[0].saveFrames, true);
+                    frames = tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([], mmcifDic.result.blocks[0].saveFrames, true), ihmDic.result.blocks[0].saveFrames, true), maDic.result.blocks[0].saveFrames, true);
                     schema = (0, cif_dic_1.generateSchema)(frames);
                     return [4 /*yield*/, runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases)];
                 case 7:
@@ -68,9 +68,9 @@ function runGenerateSchemaMmcif(name, fieldNamesPath, typescript, out, moldbImpo
 }
 function runGenerateSchemaCifCore(name, fieldNamesPath, typescript, out, moldbImportPath, addAliases) {
     if (typescript === void 0) { typescript = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var cifCoreDic, cifCoreDicVersion, version, frames, imports, schema;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, ensureCifCoreDicAvailable()];
                 case 1:
@@ -82,7 +82,7 @@ function runGenerateSchemaCifCore(name, fieldNamesPath, typescript, out, moldbIm
                         throw cifCoreDic;
                     cifCoreDicVersion = getDicVersion(cifCoreDic.result.blocks[0]);
                     version = "Dictionary versions: CifCore ".concat(cifCoreDicVersion, ".");
-                    frames = (0, tslib_1.__spreadArray)([], cifCoreDic.result.blocks[0].saveFrames, true);
+                    frames = tslib_1.__spreadArray([], cifCoreDic.result.blocks[0].saveFrames, true);
                     return [4 /*yield*/, resolveImports(frames, DIC_DIR)];
                 case 3:
                     imports = _a.sent();
@@ -96,9 +96,9 @@ function runGenerateSchemaCifCore(name, fieldNamesPath, typescript, out, moldbIm
     });
 }
 function resolveImports(frames, baseDir) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var imports, _i, frames_1, d, importGet, _a, importGet_1, g, file, dic;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     imports = new Map();
@@ -124,7 +124,7 @@ function resolveImports(frames, baseDir) {
                     dic = _b.sent();
                     if (dic.isError)
                         throw dic;
-                    imports.set(file, (0, tslib_1.__spreadArray)([], dic.result.blocks[0].saveFrames, true));
+                    imports.set(file, tslib_1.__spreadArray([], dic.result.blocks[0].saveFrames, true));
                     _b.label = 4;
                 case 4:
                     _a++;
@@ -139,9 +139,9 @@ function resolveImports(frames, baseDir) {
 }
 function runGenerateSchemaDic(name, dicPath, fieldNamesPath, typescript, out, moldbImportPath, addAliases) {
     if (typescript === void 0) { typescript = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var dic, dicVersion, dicName, version, frames, imports, schema;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, (0, parser_2.parseCifText)(fs.readFileSync(dicPath, 'utf8')).run()];
                 case 1:
@@ -151,7 +151,7 @@ function runGenerateSchemaDic(name, dicPath, fieldNamesPath, typescript, out, mo
                     dicVersion = getDicVersion(dic.result.blocks[0]);
                     dicName = getDicNamespace(dic.result.blocks[0]);
                     version = "Dictionary versions: ".concat(dicName, " ").concat(dicVersion, ".");
-                    frames = (0, tslib_1.__spreadArray)([], dic.result.blocks[0].saveFrames, true);
+                    frames = tslib_1.__spreadArray([], dic.result.blocks[0].saveFrames, true);
                     return [4 /*yield*/, resolveImports(frames, path.dirname(dicPath))];
                 case 2:
                     imports = _a.sent();
@@ -166,9 +166,9 @@ function runGenerateSchemaDic(name, dicPath, fieldNamesPath, typescript, out, mo
 }
 function runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases) {
     if (typescript === void 0) { typescript = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var filter, _a, output;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     if (!fieldNamesPath) return [3 /*break*/, 2];
@@ -194,9 +194,9 @@ function runGenerateSchema(name, version, schema, fieldNamesPath, typescript, ou
     });
 }
 function getFieldNamesFilter(fieldNamesPath) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var fieldNamesStr, parsed, csvFile, fieldNamesCol, fieldNames, filter;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     fieldNamesStr = fs.readFileSync(fieldNamesPath, 'utf8');
@@ -224,7 +224,7 @@ function getFieldNamesFilter(fieldNamesPath) {
     });
 }
 function ensureMmcifDicAvailable() {
-    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*/, ensureDicAvailable(MMCIF_DIC_PATH, MMCIF_DIC_URL)];
             case 1:
@@ -234,7 +234,7 @@ function ensureMmcifDicAvailable() {
     }); });
 }
 function ensureIhmDicAvailable() {
-    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*/, ensureDicAvailable(IHM_DIC_PATH, IHM_DIC_URL)];
             case 1:
@@ -244,7 +244,7 @@ function ensureIhmDicAvailable() {
     }); });
 }
 function ensureMaDicAvailable() {
-    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*/, ensureDicAvailable(MA_DIC_PATH, MA_DIC_URL)];
             case 1:
@@ -254,8 +254,8 @@ function ensureMaDicAvailable() {
     }); });
 }
 function ensureCifCoreDicAvailable() {
-    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*/, ensureDicAvailable(CIF_CORE_DIC_PATH, CIF_CORE_DIC_URL)];
                 case 1:
@@ -272,9 +272,9 @@ function ensureCifCoreDicAvailable() {
     });
 }
 function ensureDicAvailable(dicPath, dicUrl) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var name_1, data, _a, _b, _c;
-        return (0, tslib_1.__generator)(this, function (_d) {
+        return tslib_1.__generator(this, function (_d) {
             switch (_d.label) {
                 case 0:
                     if (!(FORCE_DIC_DOWNLOAD || !fs.existsSync(dicPath))) return [3 /*break*/, 3];
@@ -394,4 +394,3 @@ if (args.name) {
         });
     }
 }
-//# sourceMappingURL=index.js.map

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

@@ -284,7 +284,7 @@ var EXTRA_ENUM_VALUES = {};
 function generateSchema(frames, imports) {
     if (imports === void 0) { imports = new Map(); }
     var tables = {};
-    var aliases = (0, tslib_1.__assign)({}, EXTRA_ALIASES);
+    var aliases = tslib_1.__assign({}, EXTRA_ALIASES);
     var categories = {};
     var links = {};
     var ctx = { categories: categories, links: links };
@@ -453,4 +453,3 @@ function generateSchema(frames, imports) {
     return { tables: tables, aliases: aliases };
 }
 exports.generateSchema = generateSchema;
-//# sourceMappingURL=cif-dic.js.map

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

@@ -155,4 +155,3 @@ function generate(name, info, schema, fields, moldataImportPath, addAliases) {
     return "".concat(header(name, info, moldataImportPath), "\n\n").concat(getTypeShorthands(schema, fields), "\n\n").concat(codeLines.join('\n'), "\n").concat(footer(name));
 }
 exports.generate = generate;
-//# sourceMappingURL=generate.js.map

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

@@ -19,4 +19,3 @@ function parseImportGet(s) {
     });
 }
 exports.parseImportGet = parseImportGet;
-//# sourceMappingURL=helper.js.map

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

@@ -61,4 +61,3 @@ function mergeFilters() {
     return mergedFilter;
 }
 exports.mergeFilters = mergeFilters;
-//# sourceMappingURL=schema.js.map

package/lib/commonjs/cli/lipid-params/index.js

@@ -7,18 +7,18 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
+var argparse = tslib_1.__importStar(require("argparse"));
+var fs = tslib_1.__importStar(require("fs"));
+var path = tslib_1.__importStar(require("path"));
+var node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
 var generic_1 = require("../../mol-data/generic");
 var LIPIDS_DIR = path.resolve(__dirname, '../../../../build/lipids/');
 var MARTINI_LIPIDS_PATH = path.resolve(LIPIDS_DIR, 'martini_lipids.itp');
 var MARTINI_LIPIDS_URL = 'http://www.cgmartini.nl/images/parameters/lipids/Collections/martini_v2.0_lipids_all_201506.itp';
 function ensureAvailable(path, url) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var name_1, data, _a, _b, _c;
-        return (0, tslib_1.__generator)(this, function (_d) {
+        return tslib_1.__generator(this, function (_d) {
             switch (_d.label) {
                 case 0:
                     if (!(FORCE_DOWNLOAD || !fs.existsSync(path))) return [3 /*break*/, 3];
@@ -43,7 +43,7 @@ function ensureAvailable(path, url) {
     });
 }
 function ensureLipidsAvailable() {
-    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(MARTINI_LIPIDS_PATH, MARTINI_LIPIDS_URL)];
             case 1:
@@ -54,9 +54,9 @@ function ensureLipidsAvailable() {
 }
 var extraLipids = ['DMPC'];
 function run(out) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var lipidsItpStr, lipids, reLipid, m, v, _i, extraLipids_1, v, lipidNames, output;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, ensureLipidsAvailable()];
                 case 1:
@@ -101,4 +101,3 @@ var FORCE_DOWNLOAD = args.forceDownload;
 run(args.out || '').catch(function (e) {
     console.error(e);
 });
-//# sourceMappingURL=index.js.map

package/lib/commonjs/cli/state-docs/index.js

@@ -7,10 +7,10 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var _ = (0, tslib_1.__importStar)(require("../../mol-plugin-state/transforms"));
+var _ = tslib_1.__importStar(require("../../mol-plugin-state/transforms"));
 var mol_state_1 = require("../../mol-state");
 var mol_util_1 = require("../../mol-util");
-var fs = (0, tslib_1.__importStar)(require("fs"));
+var fs = tslib_1.__importStar(require("fs"));
 var pd_to_md_1 = require("./pd-to-md");
 var context_1 = require("../../mol-plugin/context");
 var param_definition_1 = require("../../mol-util/param-definition");
@@ -61,4 +61,3 @@ mol_util_1.StringBuilder.write(builder, '----------------------------');
 mol_util_1.StringBuilder.newline(builder);
 transformers.forEach(function (t) { return writeTransformer(t); });
 fs.writeFileSync("docs/state/transforms.md", mol_util_1.StringBuilder.getString(builder));
-//# sourceMappingURL=index.js.map

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

@@ -77,4 +77,3 @@ function getParams(params, offset) {
     }
     return ret;
 }
-//# sourceMappingURL=pd-to-md.js.map

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

@@ -7,17 +7,17 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.downloadCif = exports.openCif = void 0;
 var tslib_1 = require("tslib");
-var util = (0, tslib_1.__importStar)(require("util"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
+var util = tslib_1.__importStar(require("util"));
+var fs = tslib_1.__importStar(require("fs"));
+var node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
 require('util.promisify').shim();
 var cif_1 = require("../../mol-io/reader/cif");
 var mol_task_1 = require("../../mol-task");
 var readFileAsync = util.promisify(fs.readFile);
 function readFile(path) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var input, data, i;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     if (!path.match(/\.bcif$/)) return [3 /*break*/, 2];
@@ -34,9 +34,9 @@ function readFile(path) {
     });
 }
 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);
@@ -51,9 +51,9 @@ function parseCif(data) {
     });
 }
 function openCif(path) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var data;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, readFile(path)];
                 case 1:
@@ -65,9 +65,9 @@ function openCif(path) {
 }
 exports.openCif = openCif;
 function downloadCif(url, isBinary) {
-    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;
-        return (0, tslib_1.__generator)(this, function (_d) {
+        return tslib_1.__generator(this, function (_d) {
             switch (_d.label) {
                 case 0: return [4 /*yield*/, (0, node_fetch_1.default)(url)];
                 case 1:
@@ -89,4 +89,3 @@ function downloadCif(url, isBinary) {
     });
 }
 exports.downloadCif = downloadCif;
-//# sourceMappingURL=helpers.js.map