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bf313073b9
This dependency pulls a 23MB dependency graph to support nodejs v<8.0 Native alternatives exist: fs.promises, and native utils/promisify Consistency: renaming readFile --> readFileAsync where changes were made.
82 lines
2.6 KiB
JavaScript
82 lines
2.6 KiB
JavaScript
#!/usr/bin/env node
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/**
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* Copyright (c) 2022-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
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*
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* @author Alexander Rose <alexander.rose@weirdbyte.de>
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* @author Paul Pillot <paul.pillot@tandemai.com>
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*/
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import * as argparse from 'argparse';
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import * as path from 'path';
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import fs from 'fs';
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const writeFileAsync = fs.promises.writeFile;
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import { DatabaseCollection } from '../../mol-data/db';
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import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
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import { DefaultDataOptions, ensureDataAvailable, readCCD } from './util';
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function extractSaccharideNames(ccd: DatabaseCollection<CCD_Schema>) {
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const saccharideNames: string[] = [];
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for (const k in ccd) {
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const { chem_comp } = ccd[k];
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const type = chem_comp.type.value(0).toUpperCase();
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if (type.includes('SACCHARIDE')) {
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saccharideNames.push(chem_comp.id.value(0));
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}
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}
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// these are extra saccharides that don't have SACCHARIDE in their type
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saccharideNames.push(
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'UMQ', // UNDECYL-MALTOSIDE, via GlyFinder
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'SQD', // SULFOQUINOVOSYLDIACYLGLYCEROL, via GlyFinder
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);
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return saccharideNames;
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}
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function writeSaccharideNamesFile(filePath: string, ionNames: string[]) {
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const output = `/**
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* Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
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*
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* Code-generated ion names params file. Names extracted from CCD components.
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*
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* @author molstar/cli/chem-comp-dict/create-saccharides
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*/
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export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
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`;
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writeFileAsync(filePath, output);
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}
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async function run(out: string, options = DefaultDataOptions) {
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await ensureDataAvailable(options);
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const ccd = await readCCD();
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const saccharideNames = extractSaccharideNames(ccd);
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if (!fs.existsSync(path.dirname(out))) {
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fs.mkdirSync(path.dirname(out));
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}
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writeSaccharideNamesFile(out, saccharideNames);
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}
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const parser = new argparse.ArgumentParser({
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add_help: true,
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description: 'Extract and save SaccharideNames from CCD.'
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});
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parser.add_argument('out', {
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help: 'Generated file output path.'
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});
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parser.add_argument('--forceDownload', '-f', {
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action: 'store_true',
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help: 'Force download of CCD and PVCD.'
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});
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parser.add_argument('--ccdUrl', '-c', {
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help: 'Fetch the CCD from a custom URL. This forces download of the CCD.',
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required: false
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});
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interface Args {
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out: string,
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forceDownload?: boolean,
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ccdUrl?: string
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}
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const args: Args = parser.parse_args();
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run(args.out, { forceDownload: args.forceDownload, ccdUrl: args.ccdUrl });
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