molstar
Version:
A comprehensive macromolecular library.
69 lines (67 loc) • 2.46 kB
JavaScript
#!/usr/bin/env node
"use strict";
/**
* Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Josh McMenemy <josh.mcmenemy@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 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 extractIonNames(ccd) {
const ionNames = [];
for (const k in ccd) {
const { chem_comp } = ccd[k];
if (chem_comp.name.value(0).toUpperCase().includes(' ION')) {
ionNames.push(chem_comp.id.value(0));
}
}
// these are extra ions that don't have ION in their name
ionNames.push('NCO', 'OHX');
return ionNames;
}
function writeIonNamesFile(filePath, ionNames) {
const output = `/**
* Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Code-generated ion names params file. Names extracted from CCD components.
*
* @author molstar/chem-comp-dict/create-ions cli
*/
export const IonNames = 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 ionNames = extractIonNames(ccd);
if (!fs_1.default.existsSync(path.dirname(out))) {
fs_1.default.mkdirSync(path.dirname(out));
}
writeIonNamesFile(out, ionNames);
}
const parser = new argparse.ArgumentParser({
add_help: true,
description: 'Extract and save IonNames 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 });