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

A comprehensive macromolecular library.

#!/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 });
const tslib_1 = require("tslib");
const argparse = tslib_1.__importStar(require("argparse"));
const util = tslib_1.__importStar(require("util"));
const fs = tslib_1.__importStar(require("fs"));
const zlib = tslib_1.__importStar(require("zlib"));
const converter_1 = require("./converter");
require('util.promisify').shim();
async function process(srcPath, outPath, configPath, filterPath) {
    const config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;
    const filter = filterPath ? fs.readFileSync(filterPath, 'utf8') : void 0;
    const res = await (0, converter_1.convert)(srcPath, srcPath.toLowerCase().indexOf('.bcif') > 0, config, filter);
    await write(outPath, res);
}
const zipAsync = util.promisify(zlib.gzip);
async function write(outPath, res) {
    const isGz = /\.gz$/i.test(outPath);
    if (isGz) {
        res = await zipAsync(res);
    }
    fs.writeFileSync(outPath, res);
}
function run(args) {
    process(args.src, args.out, args.config, args.filter);
}
const parser = new argparse.ArgumentParser({
    add_help: true,
    description: 'Convert any BCIF file to a CIF file or vice versa'
});
parser.add_argument('src', {
    help: 'Source file path'
});
parser.add_argument('out', {
    help: 'Output file 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
});
const args = parser.parse_args();
if (args) {
    run(args);
}