molstar
Version:
A comprehensive macromolecular library.
144 lines • 6.37 kB
JavaScript
;
/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.getEncodedCif = exports.readPVCD = exports.readCCD = exports.readFileAsCollection = exports.ensureDataAvailable = exports.ensureAvailable = void 0;
var tslib_1 = require("tslib");
var util = (0, tslib_1.__importStar)(require("util"));
var path = (0, tslib_1.__importStar)(require("path"));
var fs = (0, tslib_1.__importStar)(require("fs"));
var zlib = (0, tslib_1.__importStar)(require("zlib"));
var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
require('util.promisify').shim();
var readFile = util.promisify(fs.readFile);
var writeFile = util.promisify(fs.writeFile);
var mol_task_1 = require("../../mol-task");
var cif_1 = require("../../mol-io/reader/cif");
var cif_2 = require("../../mol-io/writer/cif");
var ccd_1 = require("../../mol-io/reader/cif/schema/ccd");
function ensureAvailable(path, url, forceDownload) {
if (forceDownload === void 0) { forceDownload = false; }
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var data, _a, _b, _c, _d, _e, _f;
return (0, tslib_1.__generator)(this, function (_g) {
switch (_g.label) {
case 0:
if (!(forceDownload || !fs.existsSync(path))) return [3 /*break*/, 8];
console.log("downloading " + url + "...");
return [4 /*yield*/, (0, node_fetch_1.default)(url)];
case 1:
data = _g.sent();
if (!fs.existsSync(DATA_DIR)) {
fs.mkdirSync(DATA_DIR);
}
if (!url.endsWith('.gz')) return [3 /*break*/, 4];
_a = writeFile;
_b = [path];
_d = (_c = zlib).gunzipSync;
return [4 /*yield*/, data.buffer()];
case 2: return [4 /*yield*/, _a.apply(void 0, _b.concat([_d.apply(_c, [_g.sent()])]))];
case 3:
_g.sent();
return [3 /*break*/, 7];
case 4:
_e = writeFile;
_f = [path];
return [4 /*yield*/, data.text()];
case 5: return [4 /*yield*/, _e.apply(void 0, _f.concat([_g.sent()]))];
case 6:
_g.sent();
_g.label = 7;
case 7:
console.log("done downloading " + url);
_g.label = 8;
case 8: return [2 /*return*/];
}
});
});
}
exports.ensureAvailable = ensureAvailable;
function ensureDataAvailable(forceDownload) {
if (forceDownload === void 0) { forceDownload = false; }
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, ensureAvailable(CCD_PATH, CCD_URL, forceDownload)];
case 1:
_a.sent();
return [4 /*yield*/, ensureAvailable(PVCD_PATH, PVCD_URL, forceDownload)];
case 2:
_a.sent();
return [2 /*return*/];
}
});
});
}
exports.ensureDataAvailable = ensureDataAvailable;
function readFileAsCollection(path, schema) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var parsed, _a;
return (0, tslib_1.__generator)(this, function (_b) {
switch (_b.label) {
case 0:
_a = parseCif;
return [4 /*yield*/, readFile(path, 'utf8')];
case 1: return [4 /*yield*/, _a.apply(void 0, [_b.sent()])];
case 2:
parsed = _b.sent();
return [2 /*return*/, cif_1.CIF.toDatabaseCollection(schema, parsed.result)];
}
});
});
}
exports.readFileAsCollection = readFileAsCollection;
function readCCD() {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
return (0, tslib_1.__generator)(this, function (_a) {
return [2 /*return*/, readFileAsCollection(CCD_PATH, ccd_1.CCD_Schema)];
});
});
}
exports.readCCD = readCCD;
function readPVCD() {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
return (0, tslib_1.__generator)(this, function (_a) {
return [2 /*return*/, readFileAsCollection(PVCD_PATH, ccd_1.CCD_Schema)];
});
});
}
exports.readPVCD = readPVCD;
function parseCif(data) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var comp, parsed;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
comp = cif_1.CIF.parse(data);
console.time('parse cif');
return [4 /*yield*/, comp.run(function (p) { return console.log(mol_task_1.Progress.format(p)); }, 250)];
case 1:
parsed = _a.sent();
console.timeEnd('parse cif');
if (parsed.isError)
throw parsed;
return [2 /*return*/, parsed];
}
});
});
}
function getEncodedCif(name, database, binary) {
if (binary === void 0) { binary = false; }
var encoder = cif_2.CifWriter.createEncoder({ binary: binary, encoderName: 'mol*' });
cif_2.CifWriter.Encoder.writeDatabase(encoder, name, database);
return encoder.getData();
}
exports.getEncodedCif = getEncodedCif;
var DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/data');
var CCD_PATH = path.join(DATA_DIR, 'components.cif');
var PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
var CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif';
var PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';
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