molstar
Version:
A comprehensive macromolecular library.
73 lines (72 loc) • 3.36 kB
JavaScript
"use strict";
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
const tslib_1 = require("tslib");
const fs = tslib_1.__importStar(require("fs"));
const path = tslib_1.__importStar(require("path"));
const argparse = tslib_1.__importStar(require("argparse"));
const parallel_1 = require("./parallel");
function description() {
const exampleCfg = {
numProcesses: 1,
customProperties: {
sources: [
'wwpdb'
],
params: {
wwPDB: {
chemCompBondTablePath: './build/data/ccb.bcif'
}
}
}
};
return `Preprocess CIF files to include custom properties and convert them to BinaryCIF format.\n\nExample cfg.json: ${JSON.stringify(exampleCfg, null, 2)}`;
}
const cmdParser = new argparse.ArgumentParser({
add_help: true,
description: description()
});
cmdParser.add_argument('--input', '-i', { help: 'Input filename', required: false });
cmdParser.add_argument('--outCIF', '-oc', { help: 'Output CIF filename', required: false });
cmdParser.add_argument('--outBCIF', '-ob', { help: 'Output BinaryCIF filename', required: false });
// TODO: add back? cmdParser.addArgument(['--bulk', '-b'], { help: 'Bulk JSON ({ numProcesses?: number, entries: { source: string, cif?: string, bcif?: string }[] })', required: false });
cmdParser.add_argument('--cfg', '-c', { help: 'Config file path', required: false });
cmdParser.add_argument('--folderIn', '-fin', { help: 'Convert folder', required: false });
cmdParser.add_argument('--folderOutCIF', '-foc', { help: 'Convert folder text output', required: false });
cmdParser.add_argument('--folderOutBCIF', '-fob', { help: 'Convert folder binary output', required: false });
cmdParser.add_argument('--folderNumProcesses', '-fp', { help: 'Convert folder num processes', required: false });
const cmdArgs = cmdParser.parse_args();
if (Object.keys(cmdArgs).filter(k => cmdArgs[k] !== null).length === 0 || typeof cmdArgs.help !== 'undefined') {
cmdParser.print_help();
process.exit(0);
}
const entries = [];
let config = { numProcesses: cmdArgs.folderIn ? +(cmdArgs.folderNumProcesses || 1) : 1, customProperties: void 0 };
if (cmdArgs.input)
entries.push({ source: cmdArgs.input, cif: cmdArgs.outCIF, bcif: cmdArgs.outBCIF });
// else if (cmdArgs.bulk) runBulk(cmdArgs.bulk);
else if (cmdArgs.folderIn)
findEntries();
if (cmdArgs.cfg) {
config = JSON.parse(fs.readFileSync(cmdArgs.cfg, 'utf8'));
}
(0, parallel_1.runMaster)(config, entries);
function findEntries() {
const files = fs.readdirSync(cmdArgs.folderIn);
const cifTest = /\.cif$/;
for (const f of files) {
if (!cifTest.test(f))
continue;
entries.push({
source: path.join(cmdArgs.folderIn, f),
cif: cmdArgs.folderOutCIF ? path.join(cmdArgs.folderOutCIF, f) : void 0,
bcif: cmdArgs.folderOutBCIF ? path.join(cmdArgs.folderOutBCIF, path.parse(f).name + '.bcif') : void 0,
});
}
}
// example:
// node build\node_modules\servers\model\preprocess -i e:\test\Quick\1cbs_updated.cif -oc e:\test\mol-star\model\1cbs.cif -ob e:\test\mol-star\model\1cbs.bcif