molstar/lib/commonjs/servers/model/properties/providers/wwpdb.js

A comprehensive macromolecular library.

"use strict";
/**
 * Copyright (c) 2019-2020 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.wwPDB_chemCompAtom = exports.wwPDB_chemCompBond = void 0;
var tslib_1 = require("tslib");
var fs = tslib_1.__importStar(require("fs"));
var util = tslib_1.__importStar(require("util"));
var cif_1 = require("../../../../mol-io/reader/cif");
var util_1 = require("../../../common/util");
var mmcif_1 = require("../../../../mol-io/reader/cif/schema/mmcif");
var chem_comp_1 = require("../../../../mol-model-formats/structure/property/bonds/chem_comp");
var chem_comp_2 = require("../../../../mol-model-formats/structure/property/atoms/chem_comp");
var ccd_1 = require("../../../../mol-io/reader/cif/schema/ccd");
require('util.promisify').shim();
var readFile = util.promisify(fs.readFile);
var wwPDB_chemCompBond = function (_a) {
    var model = _a.model, params = _a.params;
    return tslib_1.__awaiter(void 0, void 0, void 0, function () {
        var table, data, entries;
        return tslib_1.__generator(this, function (_b) {
            switch (_b.label) {
                case 0: return [4 /*yield*/, getChemCompBondTable(getBondTablePath(params))];
                case 1:
                    table = _b.sent();
                    data = chem_comp_1.ComponentBond.chemCompBondFromTable(model, table);
                    entries = chem_comp_1.ComponentBond.getEntriesFromChemCompBond(data);
                    return [2 /*return*/, chem_comp_1.ComponentBond.Provider.set(model, { entries: entries, data: data })];
            }
        });
    });
};
exports.wwPDB_chemCompBond = wwPDB_chemCompBond;
function read(path) {
    return tslib_1.__awaiter(this, void 0, void 0, function () {
        var _a, _b;
        return tslib_1.__generator(this, function (_c) {
            switch (_c.label) {
                case 0:
                    if (!path.endsWith('.bcif')) return [3 /*break*/, 2];
                    _b = Uint8Array.bind;
                    return [4 /*yield*/, readFile(path)];
                case 1:
                    _a = new (_b.apply(Uint8Array, [void 0, _c.sent()]))();
                    return [3 /*break*/, 3];
                case 2:
                    _a = readFile(path, 'utf8');
                    _c.label = 3;
                case 3: return [2 /*return*/, _a];
            }
        });
    });
}
var chemCompBondTable;
function getChemCompBondTable(path) {
    return tslib_1.__awaiter(this, void 0, void 0, function () {
        var parsed, _a, _b, table;
        return tslib_1.__generator(this, function (_c) {
            switch (_c.label) {
                case 0:
                    if (!!chemCompBondTable) return [3 /*break*/, 3];
                    _b = (_a = cif_1.CIF).parse;
                    return [4 /*yield*/, read(path)];
                case 1: return [4 /*yield*/, _b.apply(_a, [_c.sent()]).run()];
                case 2:
                    parsed = _c.sent();
                    if (parsed.isError)
                        throw new Error(parsed.toString());
                    table = cif_1.CIF.toDatabase(mmcif_1.mmCIF_Schema, parsed.result.blocks[0]);
                    chemCompBondTable = table.chem_comp_bond;
                    _c.label = 3;
                case 3: return [2 /*return*/, chemCompBondTable];
            }
        });
    });
}
function getBondTablePath(params) {
    var path = (0, util_1.getParam)(params, 'wwPDB', 'chemCompBondTablePath');
    if (!path)
        throw new Error("wwPDB 'chemCompBondTablePath' not set!");
    return path;
}
var wwPDB_chemCompAtom = function (_a) {
    var model = _a.model, params = _a.params;
    return tslib_1.__awaiter(void 0, void 0, void 0, function () {
        var table, data, entries;
        return tslib_1.__generator(this, function (_b) {
            switch (_b.label) {
                case 0: return [4 /*yield*/, getChemCompAtomTable(getAtomTablePath(params))];
                case 1:
                    table = _b.sent();
                    data = chem_comp_2.ComponentAtom.chemCompAtomFromTable(model, table);
                    entries = chem_comp_2.ComponentAtom.getEntriesFromChemCompAtom(data);
                    return [2 /*return*/, chem_comp_2.ComponentAtom.Provider.set(model, { entries: entries, data: data })];
            }
        });
    });
};
exports.wwPDB_chemCompAtom = wwPDB_chemCompAtom;
var chemCompAtomTable;
function getChemCompAtomTable(path) {
    return tslib_1.__awaiter(this, void 0, void 0, function () {
        var parsed, _a, _b, table;
        return tslib_1.__generator(this, function (_c) {
            switch (_c.label) {
                case 0:
                    if (!!chemCompAtomTable) return [3 /*break*/, 3];
                    _b = (_a = cif_1.CIF).parse;
                    return [4 /*yield*/, read(path)];
                case 1: return [4 /*yield*/, _b.apply(_a, [_c.sent()]).run()];
                case 2:
                    parsed = _c.sent();
                    if (parsed.isError)
                        throw new Error(parsed.toString());
                    table = cif_1.CIF.toDatabase(ccd_1.CCD_Schema, parsed.result.blocks[0]);
                    chemCompAtomTable = table.chem_comp_atom;
                    _c.label = 3;
                case 3: return [2 /*return*/, chemCompAtomTable];
            }
        });
    });
}
function getAtomTablePath(params) {
    var path = (0, util_1.getParam)(params, 'wwPDB', 'chemCompAtomTablePath');
    if (!path)
        throw new Error("wwPDB 'chemCompAtomTablePath' not set!");
    return path;
}