molstar
Version:
A comprehensive macromolecular library.
59 lines (58 loc) • 2.64 kB
JavaScript
;
/**
* Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.PdbFormat = void 0;
exports.trajectoryFromPDB = trajectoryFromPDB;
const to_cif_1 = require("./pdb/to-cif");
const mol_task_1 = require("../../mol-task");
const mmcif_1 = require("./mmcif");
const parser_1 = require("./basic/parser");
const db_1 = require("../../mol-data/db");
const partial_charge_1 = require("./property/partial-charge");
const schema_1 = require("./basic/schema");
var PdbFormat;
(function (PdbFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'pdb';
}
PdbFormat.is = is;
function create(pdb) {
return { kind: 'pdb', name: pdb.id || '', data: pdb };
}
PdbFormat.create = create;
})(PdbFormat || (exports.PdbFormat = PdbFormat = {}));
function trajectoryFromPDB(pdb) {
return mol_task_1.Task.create('Parse PDB', async (ctx) => {
var _a;
await ctx.update('Converting to mmCIF');
const cif = await (0, to_cif_1.pdbToMmCif)(pdb);
const format = mmcif_1.MmcifFormat.fromFrame(cif, undefined, PdbFormat.create(pdb));
const basic = (0, schema_1.createBasic)(format.data.db, true);
const models = await (0, parser_1.createModels)(basic, format, ctx);
const partial_charge = (_a = cif.categories['atom_site']) === null || _a === void 0 ? void 0 : _a.getField('partial_charge');
if (partial_charge) {
// TODO works only for single, unsorted model, to work generally
// would need to do model splitting again
if (models.frameCount === 1) {
const first = models.representative;
const srcIndex = first.atomicHierarchy.atomSourceIndex;
const isIdentity = db_1.Column.isIdentity(srcIndex);
const srcIndexArray = isIdentity ? void 0 : srcIndex.toArray({ array: Int32Array });
const q = partial_charge.toFloatArray();
const partialCharge = srcIndexArray
? db_1.Column.ofFloatArray(db_1.Column.mapToArray(srcIndex, i => q[i], Float32Array))
: db_1.Column.ofFloatArray(q);
partial_charge_1.AtomPartialCharge.Provider.set(first, {
data: partialCharge,
type: 'GASTEIGER' // from PDBQT
});
}
}
return models;
});
}