molstar
Version:
A comprehensive macromolecular library.
90 lines (89 loc) • 3.2 kB
JavaScript
;
/**
* Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.jsonCifToMolfile = jsonCifToMolfile;
const model_1 = require("../../extensions/json-cif/model");
function padLeft(v, n = 3) {
let s = `${v}`;
while (s.length < n)
s = ' ' + s;
return s;
}
function padRight(v, n = 3) {
let s = `${v}`;
while (s.length < n)
s = s + ' ';
return s;
}
function mapMolChage(v) {
switch (v) {
case 3: return 1;
case 2: return 2;
case 1: return 3;
case -1: return 5;
case -2: return 6;
case -3: return 7;
default: return 0;
}
}
function mapMolBondOrder(order, type) {
if (type !== 'covale')
return 8;
switch (order) {
case 'sing': return 1;
case 'doub': return 2;
case 'trip': return 3;
case 'arom': return 4;
default: return 8;
}
}
function jsonCifToMolfile(data, options) {
// The method works in the sense that Mol* can re-open the file.
// For production use, this will likely need more testing and tweaks (e.g., support for M CHG property).
var _a, _b;
if (data.categories.atom_site === undefined || data.categories.molstar_bond_site === undefined) {
throw new Error('The data block must contain atom_site and molstar_bond_site categories.');
}
const { atom_site: _atoms, molstar_bond_site: _bonds } = data.categories;
const atoms = (0, model_1.getJSONCifCategory)(data, 'atom_site');
const bonds = (0, model_1.getJSONCifCategory)(data, 'molstar_bond_site');
const lines = [
`${(_a = options === null || options === void 0 ? void 0 : options.name) !== null && _a !== void 0 ? _a : 'mol'}`,
' Molstar 3D',
(_b = options === null || options === void 0 ? void 0 : options.comment) !== null && _b !== void 0 ? _b : '',
`${padLeft(atoms.rows.length)}${padLeft(bonds.rows.length)} 0 0 0 0 0 0 0 0 V2000`,
];
const atomIdToIndex = new Map();
for (let i = 0; i < atoms.rows.length; ++i) {
const a = atoms.rows[i];
const { id, Cartn_x, Cartn_y, Cartn_z, type_symbol, pdbx_formal_charge } = a;
atomIdToIndex.set(id, i + 1);
const fields = [
padLeft(Cartn_x.toFixed(4), 10),
padLeft(Cartn_y.toFixed(4), 10),
padLeft(Cartn_z.toFixed(4), 10),
' ',
padRight(type_symbol, 2),
' 0',
padLeft(mapMolChage(pdbx_formal_charge), 3),
' 0 0 0 0 0 0 0 0 0 0',
];
lines.push(fields.join(''));
}
for (const b of bonds.rows) {
const { atom_id_1, atom_id_2, value_order, type_id } = b;
const fields = [
padLeft(atomIdToIndex.get(atom_id_1), 3),
padLeft(atomIdToIndex.get(atom_id_2), 3),
padLeft(mapMolBondOrder(value_order, type_id), 3),
' 0 0 0 0',
];
lines.push(fields.join(''));
}
lines.push('M END');
return lines.join('\n');
}