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

A comprehensive macromolecular library.

#!/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 });
const tslib_1 = require("tslib");
const argparse = tslib_1.__importStar(require("argparse"));
const path = tslib_1.__importStar(require("path"));
const util_1 = tslib_1.__importDefault(require("util"));
const fs_1 = tslib_1.__importDefault(require("fs"));
require('util.promisify').shim();
const writeFile = util_1.default.promisify(fs_1.default.writeFile);
const util_2 = require("./util");
function extractSaccharideNames(ccd) {
    const saccharideNames = [];
    for (const k in ccd) {
        const { chem_comp } = ccd[k];
        const 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) {
    const output = `/**
 * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * Code-generated ion names params file. Names extracted from CCD components.
 *
 * @author molstar/cli/chem-comp-dict/create-saccharides
 */

export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
`;
    writeFile(filePath, output);
}
async function run(out, options = util_2.DefaultDataOptions) {
    await (0, util_2.ensureDataAvailable)(options);
    const ccd = await (0, util_2.readCCD)();
    const saccharideNames = extractSaccharideNames(ccd);
    if (!fs_1.default.existsSync(path.dirname(out))) {
        fs_1.default.mkdirSync(path.dirname(out));
    }
    writeSaccharideNamesFile(out, saccharideNames);
}
const 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.'
});
parser.add_argument('--ccdUrl', '-c', {
    help: 'Fetch the CCD from a custom URL. This forces download of the CCD.',
    required: false
});
const args = parser.parse_args();
run(args.out, { forceDownload: args.forceDownload, ccdUrl: args.ccdUrl });