molstar 3.0.0-dev.7 → 3.0.1

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

@@ -1,187 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-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 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");
-function showProgress(p) {
-    process.stdout.write("\r".concat(new Array(80).join(' ')));
-    process.stdout.write("\r".concat(mol_task_1.Progress.format(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 () {
-        var isGz, input, str, data, _a;
-        return (0, tslib_1.__generator)(this, function (_b) {
-            switch (_b.label) {
-                case 0:
-                    isGz = /\.gz$/i.test(filename);
-                    if (!filename.match(/\.bcif/)) return [3 /*break*/, 5];
-                    return [4 /*yield*/, readFileAsync(filename)];
-                case 1:
-                    input = _b.sent();
-                    if (!isGz) return [3 /*break*/, 3];
-                    return [4 /*yield*/, unzipAsync(input)];
-                case 2:
-                    input = _b.sent();
-                    _b.label = 3;
-                case 3: return [4 /*yield*/, cif_1.CIF.parseBinary(new Uint8Array(input)).runInContext(ctx)];
-                case 4: return [2 /*return*/, _b.sent()];
-                case 5:
-                    str = void 0;
-                    if (!isGz) return [3 /*break*/, 8];
-                    _a = unzipAsync;
-                    return [4 /*yield*/, readFileAsync(filename)];
-                case 6: return [4 /*yield*/, _a.apply(void 0, [_b.sent()])];
-                case 7:
-                    data = _b.sent();
-                    str = data.toString('utf8');
-                    return [3 /*break*/, 10];
-                case 8: return [4 /*yield*/, readFileAsync(filename, 'utf8')];
-                case 9:
-                    str = _b.sent();
-                    _b.label = 10;
-                case 10: return [4 /*yield*/, cif_1.CIF.parseText(str).runInContext(ctx)];
-                case 11: return [2 /*return*/, _b.sent()];
-            }
-        });
-    });
-}
-function getCIF(ctx, filename) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var parsed;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, readFile(ctx, filename)];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError) {
-                        throw new Error(parsed.toString());
-                    }
-                    return [2 /*return*/, parsed.result];
-            }
-        });
-    });
-}
-function getCategoryInstanceProvider(cat, fields) {
-    return {
-        name: cat.name,
-        instance: function () { return cif_2.CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount }); }
-    };
-}
-function classify(name, field) {
-    var type = (0, cif_1.getCifFieldType)(field);
-    if (type['@type'] === 'str') {
-        return { name: name, type: 0 /* Str */, value: field.str, valueKind: field.valueKind };
-    }
-    else if (type['@type'] === 'float') {
-        var encoder = (0, binary_cif_1.classifyFloatArray)(field.toFloatArray({ array: Float64Array }));
-        return cif_2.CifWriter.Field.float(name, field.float, { valueKind: field.valueKind, encoder: encoder, typedArray: Float64Array });
-    }
-    else {
-        var encoder = (0, binary_cif_1.classifyIntArray)(field.toIntArray({ array: Int32Array }));
-        return cif_2.CifWriter.Field.int(name, field.int, { valueKind: field.valueKind, encoder: encoder, typedArray: Int32Array });
-    }
-}
-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 () {
-        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) {
-            switch (_k.label) {
-                case 0:
-                    encodingProvider = hints
-                        ? cif_2.CifWriter.createEncodingProviderFromJsonConfig(hints)
-                        : { get: function (c, f) { return void 0; } };
-                    return [4 /*yield*/, getCIF(ctx, path)];
-                case 1:
-                    cif = _k.sent();
-                    encoder = cif_2.CifWriter.createEncoder({
-                        binary: !asText,
-                        encoderName: 'mol*/ciftools cif2bcif',
-                        binaryAutoClassifyEncoding: true,
-                        binaryEncodingPovider: encodingProvider
-                    });
-                    if (filter) {
-                        encoder.setFilter(encoder_1.Category.filterOf(filter));
-                    }
-                    maxProgress = 0;
-                    for (_i = 0, _a = cif.blocks; _i < _a.length; _i++) {
-                        b = _a[_i];
-                        maxProgress += b.categoryNames.length;
-                        for (_b = 0, _c = b.categoryNames; _b < _c.length; _b++) {
-                            c = _c[_b];
-                            maxProgress += b.categories[c].fieldNames.length;
-                        }
-                    }
-                    current = 0;
-                    _d = 0, _e = cif.blocks;
-                    _k.label = 2;
-                case 2:
-                    if (!(_d < _e.length)) return [3 /*break*/, 11];
-                    b = _e[_d];
-                    encoder.startDataBlock(b.header);
-                    _f = 0, _g = b.categoryNames;
-                    _k.label = 3;
-                case 3:
-                    if (!(_f < _g.length)) return [3 /*break*/, 10];
-                    c = _g[_f];
-                    cat = b.categories[c];
-                    fields = [];
-                    _h = 0, _j = cat.fieldNames;
-                    _k.label = 4;
-                case 4:
-                    if (!(_h < _j.length)) return [3 /*break*/, 7];
-                    f = _j[_h];
-                    fields.push(classify(f, cat.getField(f)));
-                    current++;
-                    if (!ctx.shouldUpdate) return [3 /*break*/, 6];
-                    return [4 /*yield*/, ctx.update({ message: 'Encoding...', current: current, max: maxProgress })];
-                case 5:
-                    _k.sent();
-                    _k.label = 6;
-                case 6:
-                    _h++;
-                    return [3 /*break*/, 4];
-                case 7:
-                    encoder.writeCategory(getCategoryInstanceProvider(b.categories[c], fields));
-                    current++;
-                    if (!ctx.shouldUpdate) return [3 /*break*/, 9];
-                    return [4 /*yield*/, ctx.update({ message: 'Encoding...', current: current, max: maxProgress })];
-                case 8:
-                    _k.sent();
-                    _k.label = 9;
-                case 9:
-                    _f++;
-                    return [3 /*break*/, 3];
-                case 10:
-                    _d++;
-                    return [3 /*break*/, 2];
-                case 11: return [4 /*yield*/, ctx.update('Exporting...')];
-                case 12:
-                    _k.sent();
-                    ret = encoder.getData();
-                    return [4 /*yield*/, ctx.update('Done.\n')];
-                case 13:
-                    _k.sent();
-                    return [2 /*return*/, ret];
-            }
-        });
-    }); }).run(showProgress, 250);
-}
-exports.convert = convert;
-//# sourceMappingURL=converter.js.map

package/lib/commonjs/cli/cif2bcif/index.d.ts

@@ -1,8 +0,0 @@
-#!/usr/bin/env node
-/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-export {};

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

@@ -1,81 +0,0 @@
-#!/usr/bin/env node
-"use strict";
-/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-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 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 () {
-        var config, filter, res;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;
-                    filter = filterPath ? fs.readFileSync(filterPath, 'utf8') : void 0;
-                    return [4 /*yield*/, (0, converter_1.convert)(srcPath, false, config, filter)];
-                case 1:
-                    res = _a.sent();
-                    return [4 /*yield*/, write(outPath, res)];
-                case 2:
-                    _a.sent();
-                    return [2 /*return*/];
-            }
-        });
-    });
-}
-var zipAsync = util.promisify(zlib.gzip);
-function write(outPath, res) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var isGz;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    isGz = /\.gz$/i.test(outPath);
-                    if (!isGz) return [3 /*break*/, 2];
-                    return [4 /*yield*/, zipAsync(res)];
-                case 1:
-                    res = _a.sent();
-                    _a.label = 2;
-                case 2:
-                    fs.writeFileSync(outPath, res);
-                    return [2 /*return*/];
-            }
-        });
-    });
-}
-function run(args) {
-    process(args.src, args.out, args.config, args.filter);
-}
-var parser = new argparse.ArgumentParser({
-    add_help: true,
-    description: 'Convert any CIF file to a BCIF file'
-});
-parser.add_argument('src', {
-    help: 'Source CIF path'
-});
-parser.add_argument('out', {
-    help: 'Output BCIF path'
-});
-parser.add_argument('-c', '--config', {
-    help: 'Optional encoding strategy/precision config path',
-    required: false
-});
-parser.add_argument('-f', '--filter', {
-    help: 'Optional filter whitelist/blacklist path',
-    required: false
-});
-var args = parser.parse_args();
-if (args) {
-    run(args);
-}
-//# sourceMappingURL=index.js.map

package/lib/commonjs/cli/cifschema/index.d.ts

@@ -1,7 +0,0 @@
-#!/usr/bin/env node
-/**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-export {};

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

@@ -1,397 +0,0 @@
-#!/usr/bin/env node
-"use strict";
-/**
- * Copyright (c) 2017-2021 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 = (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 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");
-var generate_1 = require("./util/generate");
-var helper_1 = require("./util/helper");
-function getDicVersion(block) {
-    return block.categories.dictionary.getField('version').str(0);
-}
-function getDicNamespace(block) {
-    return block.categories.dictionary.getField('namespace').str(0);
-}
-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 () {
-        var mmcifDic, ihmDic, maDic, mmcifDicVersion, ihmDicVersion, maDicVersion, version, frames, schema;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, ensureMmcifDicAvailable()];
-                case 1:
-                    _a.sent();
-                    return [4 /*yield*/, (0, parser_2.parseCifText)(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run()];
-                case 2:
-                    mmcifDic = _a.sent();
-                    if (mmcifDic.isError)
-                        throw mmcifDic;
-                    return [4 /*yield*/, ensureIhmDicAvailable()];
-                case 3:
-                    _a.sent();
-                    return [4 /*yield*/, (0, parser_2.parseCifText)(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run()];
-                case 4:
-                    ihmDic = _a.sent();
-                    if (ihmDic.isError)
-                        throw ihmDic;
-                    return [4 /*yield*/, ensureMaDicAvailable()];
-                case 5:
-                    _a.sent();
-                    return [4 /*yield*/, (0, parser_2.parseCifText)(fs.readFileSync(MA_DIC_PATH, 'utf8')).run()];
-                case 6:
-                    maDic = _a.sent();
-                    if (maDic.isError)
-                        throw maDic;
-                    mmcifDicVersion = getDicVersion(mmcifDic.result.blocks[0]);
-                    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);
-                    schema = (0, cif_dic_1.generateSchema)(frames);
-                    return [4 /*yield*/, runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases)];
-                case 7:
-                    _a.sent();
-                    return [2 /*return*/];
-            }
-        });
-    });
-}
-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 () {
-        var cifCoreDic, cifCoreDicVersion, version, frames, imports, schema;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, ensureCifCoreDicAvailable()];
-                case 1:
-                    _a.sent();
-                    return [4 /*yield*/, (0, parser_2.parseCifText)(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run()];
-                case 2:
-                    cifCoreDic = _a.sent();
-                    if (cifCoreDic.isError)
-                        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);
-                    return [4 /*yield*/, resolveImports(frames, DIC_DIR)];
-                case 3:
-                    imports = _a.sent();
-                    schema = (0, cif_dic_1.generateSchema)(frames, imports);
-                    return [4 /*yield*/, runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases)];
-                case 4:
-                    _a.sent();
-                    return [2 /*return*/];
-            }
-        });
-    });
-}
-function resolveImports(frames, baseDir) {
-    return (0, 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) {
-            switch (_b.label) {
-                case 0:
-                    imports = new Map();
-                    _i = 0, frames_1 = frames;
-                    _b.label = 1;
-                case 1:
-                    if (!(_i < frames_1.length)) return [3 /*break*/, 6];
-                    d = frames_1[_i];
-                    if (!('import' in d.categories)) return [3 /*break*/, 5];
-                    importGet = (0, helper_1.parseImportGet)(d.categories['import'].getField('get').str(0));
-                    _a = 0, importGet_1 = importGet;
-                    _b.label = 2;
-                case 2:
-                    if (!(_a < importGet_1.length)) return [3 /*break*/, 5];
-                    g = importGet_1[_a];
-                    file = g.file;
-                    if (!file)
-                        return [3 /*break*/, 4];
-                    if (imports.has(file))
-                        return [3 /*break*/, 4];
-                    return [4 /*yield*/, (0, parser_2.parseCifText)(fs.readFileSync(path.join(baseDir, file), 'utf8')).run()];
-                case 3:
-                    dic = _b.sent();
-                    if (dic.isError)
-                        throw dic;
-                    imports.set(file, (0, tslib_1.__spreadArray)([], dic.result.blocks[0].saveFrames, true));
-                    _b.label = 4;
-                case 4:
-                    _a++;
-                    return [3 /*break*/, 2];
-                case 5:
-                    _i++;
-                    return [3 /*break*/, 1];
-                case 6: return [2 /*return*/, imports];
-            }
-        });
-    });
-}
-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 () {
-        var dic, dicVersion, dicName, version, frames, imports, schema;
-        return (0, 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:
-                    dic = _a.sent();
-                    if (dic.isError)
-                        throw dic;
-                    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);
-                    return [4 /*yield*/, resolveImports(frames, path.dirname(dicPath))];
-                case 2:
-                    imports = _a.sent();
-                    schema = (0, cif_dic_1.generateSchema)(frames, imports);
-                    return [4 /*yield*/, runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases)];
-                case 3:
-                    _a.sent();
-                    return [2 /*return*/];
-            }
-        });
-    });
-}
-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 () {
-        var filter, _a, output;
-        return (0, tslib_1.__generator)(this, function (_b) {
-            switch (_b.label) {
-                case 0:
-                    if (!fieldNamesPath) return [3 /*break*/, 2];
-                    return [4 /*yield*/, getFieldNamesFilter(fieldNamesPath)];
-                case 1:
-                    _a = _b.sent();
-                    return [3 /*break*/, 3];
-                case 2:
-                    _a = undefined;
-                    _b.label = 3;
-                case 3:
-                    filter = _a;
-                    output = typescript ? (0, generate_1.generate)(name, version, schema, filter, moldbImportPath, addAliases) : JSON.stringify(schema, undefined, 4);
-                    if (out) {
-                        fs.writeFileSync(out, output);
-                    }
-                    else {
-                        console.log(output);
-                    }
-                    return [2 /*return*/];
-            }
-        });
-    });
-}
-function getFieldNamesFilter(fieldNamesPath) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var fieldNamesStr, parsed, csvFile, fieldNamesCol, fieldNames, filter;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    fieldNamesStr = fs.readFileSync(fieldNamesPath, 'utf8');
-                    return [4 /*yield*/, (0, parser_1.parseCsv)(fieldNamesStr, { noColumnNames: true }).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError)
-                        throw parser.error;
-                    csvFile = parsed.result;
-                    fieldNamesCol = csvFile.table.getColumn('0');
-                    if (!fieldNamesCol)
-                        throw new Error('error getting fields columns');
-                    fieldNames = fieldNamesCol.toStringArray();
-                    filter = {};
-                    fieldNames.forEach(function (name, i) {
-                        var _a = name.split('.'), category = _a[0], field = _a[1];
-                        // console.log(category, field)
-                        if (!filter[category])
-                            filter[category] = {};
-                        filter[category][field] = true;
-                    });
-                    return [2 /*return*/, filter];
-            }
-        });
-    });
-}
-function ensureMmcifDicAvailable() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () { return (0, tslib_1.__generator)(this, function (_a) {
-        switch (_a.label) {
-            case 0: return [4 /*yield*/, ensureDicAvailable(MMCIF_DIC_PATH, MMCIF_DIC_URL)];
-            case 1:
-                _a.sent();
-                return [2 /*return*/];
-        }
-    }); });
-}
-function ensureIhmDicAvailable() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () { return (0, tslib_1.__generator)(this, function (_a) {
-        switch (_a.label) {
-            case 0: return [4 /*yield*/, ensureDicAvailable(IHM_DIC_PATH, IHM_DIC_URL)];
-            case 1:
-                _a.sent();
-                return [2 /*return*/];
-        }
-    }); });
-}
-function ensureMaDicAvailable() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () { return (0, tslib_1.__generator)(this, function (_a) {
-        switch (_a.label) {
-            case 0: return [4 /*yield*/, ensureDicAvailable(MA_DIC_PATH, MA_DIC_URL)];
-            case 1:
-                _a.sent();
-                return [2 /*return*/];
-        }
-    }); });
-}
-function ensureCifCoreDicAvailable() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, 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:
-                    _a.sent();
-                    return [4 /*yield*/, ensureDicAvailable(CIF_CORE_ENUM_PATH, CIF_CORE_ENUM_URL)];
-                case 2:
-                    _a.sent();
-                    return [4 /*yield*/, ensureDicAvailable(CIF_CORE_ATTR_PATH, CIF_CORE_ATTR_URL)];
-                case 3:
-                    _a.sent();
-                    return [2 /*return*/];
-            }
-        });
-    });
-}
-function ensureDicAvailable(dicPath, dicUrl) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var name_1, data, _a, _b, _c;
-        return (0, tslib_1.__generator)(this, function (_d) {
-            switch (_d.label) {
-                case 0:
-                    if (!(FORCE_DIC_DOWNLOAD || !fs.existsSync(dicPath))) return [3 /*break*/, 3];
-                    name_1 = dicUrl.substr(dicUrl.lastIndexOf('/') + 1);
-                    console.log("downloading ".concat(name_1, "..."));
-                    return [4 /*yield*/, (0, node_fetch_1.default)(dicUrl)];
-                case 1:
-                    data = _d.sent();
-                    if (!fs.existsSync(DIC_DIR)) {
-                        fs.mkdirSync(DIC_DIR);
-                    }
-                    _b = (_a = fs).writeFileSync;
-                    _c = [dicPath];
-                    return [4 /*yield*/, data.text()];
-                case 2:
-                    _b.apply(_a, _c.concat([_d.sent()]));
-                    console.log("done downloading ".concat(name_1));
-                    _d.label = 3;
-                case 3: return [2 /*return*/];
-            }
-        });
-    });
-}
-var DIC_DIR = path.resolve(__dirname, '../../../../build/dics/');
-var MMCIF_DIC_PATH = "".concat(DIC_DIR, "/mmcif_pdbx_v50.dic");
-var MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic';
-var IHM_DIC_PATH = "".concat(DIC_DIR, "/ihm-extension.dic");
-var IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic';
-var MA_DIC_PATH = "".concat(DIC_DIR, "/ma-extension.dic");
-var MA_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/MA-dictionary/master/mmcif_ma.dic';
-var CIF_CORE_DIC_PATH = "".concat(DIC_DIR, "/cif_core.dic");
-var CIF_CORE_DIC_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic';
-var CIF_CORE_ENUM_PATH = "".concat(DIC_DIR, "/templ_enum.cif");
-var CIF_CORE_ENUM_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_enum.cif';
-var CIF_CORE_ATTR_PATH = "".concat(DIC_DIR, "/templ_attr.cif");
-var CIF_CORE_ATTR_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_attr.cif';
-var parser = new argparse.ArgumentParser({
-    add_help: true,
-    description: 'Create schema from mmcif dictionary (v50 plus IHM and entity_branch extensions, downloaded from wwPDB)'
-});
-parser.add_argument('--preset', '-p', {
-    default: '',
-    choices: ['', 'mmCIF', 'CCD', 'BIRD', 'CifCore'],
-    help: 'Preset name'
-});
-parser.add_argument('--name', '-n', {
-    default: '',
-    help: 'Schema name'
-});
-parser.add_argument('--out', '-o', {
-    help: 'Generated schema output path, if not given printed to stdout'
-});
-parser.add_argument('--targetFormat', '-tf', {
-    default: 'typescript-molstar',
-    choices: ['typescript-molstar', 'json-internal'],
-    help: 'Target format'
-});
-parser.add_argument('--dicPath', '-d', {
-    default: '',
-    help: 'Path to dictionary'
-});
-parser.add_argument('--fieldNamesPath', '-fn', {
-    default: '',
-    help: 'Field names to include'
-});
-parser.add_argument('--forceDicDownload', '-f', {
-    action: 'store_true',
-    help: 'Force download of dictionaries'
-});
-parser.add_argument('--moldataImportPath', '-mip', {
-    default: 'molstar/lib/mol-data',
-    help: 'mol-data import path (for typescript target only)'
-});
-parser.add_argument('--addAliases', '-aa', {
-    action: 'store_true',
-    help: 'Add field name/path aliases'
-});
-var args = parser.parse_args();
-var FORCE_DIC_DOWNLOAD = args.forceDicDownload;
-switch (args.preset) {
-    case 'mmCIF':
-        args.name = 'mmCIF';
-        args.dic = 'mmCIF';
-        args.fieldNamesPath = path.resolve(__dirname, '../../../../data/cif-field-names/mmcif-field-names.csv');
-        break;
-    case 'CCD':
-        args.name = 'CCD';
-        args.dic = 'mmCIF';
-        args.fieldNamesPath = path.resolve(__dirname, '../../../../data/cif-field-names/ccd-field-names.csv');
-        break;
-    case 'BIRD':
-        args.name = 'BIRD';
-        args.dic = 'mmCIF';
-        args.fieldNamesPath = path.resolve(__dirname, '../../../../data/cif-field-names/bird-field-names.csv');
-        break;
-    case 'CifCore':
-        args.name = 'CifCore';
-        args.dic = 'CifCore';
-        args.fieldNamesPath = path.resolve(__dirname, '../../../../data/cif-field-names/cif-core-field-names.csv');
-        break;
-}
-if (args.name) {
-    var typescript = args.targetFormat === 'typescript-molstar';
-    if (args.dicPath) {
-        runGenerateSchemaDic(args.name, args.dicPath, args.fieldNamesPath, typescript, args.out, args.moldataImportPath, args.addAliases).catch(function (e) {
-            console.error(e);
-        });
-    }
-    else if (args.dic === 'mmCIF') {
-        runGenerateSchemaMmcif(args.name, args.fieldNamesPath, typescript, args.out, args.moldataImportPath, args.addAliases).catch(function (e) {
-            console.error(e);
-        });
-    }
-    else if (args.dic === 'CifCore') {
-        runGenerateSchemaCifCore(args.name, args.fieldNamesPath, typescript, args.out, args.moldataImportPath, args.addAliases).catch(function (e) {
-            console.error(e);
-        });
-    }
-}
-//# sourceMappingURL=index.js.map