molstar
Version:
A comprehensive macromolecular library.
70 lines (69 loc) • 2.77 kB
JavaScript
/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import * as util from 'util';
import * as path from 'path';
import * as fs from 'fs';
import * as zlib from 'zlib';
import fetch from 'node-fetch';
require('util.promisify').shim();
const readFile = util.promisify(fs.readFile);
const writeFile = util.promisify(fs.writeFile);
import { Progress } from '../../mol-task';
import { CIF } from '../../mol-io/reader/cif';
import { CifWriter } from '../../mol-io/writer/cif';
import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
export async function ensureAvailable(path, url, forceDownload = false) {
if (forceDownload || !fs.existsSync(path)) {
console.log(`downloading ${url}...`);
const data = await fetch(url);
if (!fs.existsSync(DATA_DIR)) {
fs.mkdirSync(DATA_DIR);
}
if (url.endsWith('.gz')) {
await writeFile(path, zlib.gunzipSync(await data.buffer()));
}
else {
await writeFile(path, await data.text());
}
console.log(`done downloading ${url}`);
}
}
export async function ensureDataAvailable(options) {
await ensureAvailable(CCD_PATH, options.ccdUrl || CCD_URL, !!options.ccdUrl || options.forceDownload);
await ensureAvailable(PVCD_PATH, options.pvcdUrl || PVCD_URL, !!options.pvcdUrl || options.forceDownload);
}
export async function readFileAsCollection(path, schema) {
const parsed = await parseCif(await readFile(path, 'utf8'));
return CIF.toDatabaseCollection(schema, parsed.result);
}
export async function readCCD() {
return readFileAsCollection(CCD_PATH, CCD_Schema);
}
export async function readPVCD() {
return readFileAsCollection(PVCD_PATH, CCD_Schema);
}
async function parseCif(data) {
const comp = CIF.parse(data);
console.time('parse cif');
const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
console.timeEnd('parse cif');
if (parsed.isError)
throw parsed;
return parsed;
}
export function getEncodedCif(name, database, binary = false) {
const encoder = CifWriter.createEncoder({ binary, encoderName: 'mol*' });
CifWriter.Encoder.writeDatabase(encoder, name, database);
return encoder.getData();
}
export const DefaultDataOptions = {
forceDownload: false
};
const DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/data');
const CCD_PATH = path.join(DATA_DIR, 'components.cif');
const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
const CCD_URL = 'https://files.wwpdb.org/pub/pdb/data/monomers/components.cif';
const PVCD_URL = 'https://files.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';