molstar
Version:
A comprehensive macromolecular library.
78 lines • 4.2 kB
JavaScript
;
/**
* Copyright (c) 2020 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.trajectoryFromCube = void 0;
var tslib_1 = require("tslib");
var db_1 = require("../../mol-data/db");
var types_1 = require("../../mol-model/structure/model/types");
var mol_task_1 = require("../../mol-task");
var parser_1 = require("./basic/parser");
var schema_1 = require("./basic/schema");
var component_1 = require("./common/component");
var entity_1 = require("./common/entity");
function getModels(cube, ctx) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var atoms, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basics;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
atoms = cube.atoms;
MOL = db_1.Column.ofConst('MOL', cube.atoms.count, db_1.Column.Schema.str);
A = db_1.Column.ofConst('A', cube.atoms.count, db_1.Column.Schema.str);
type_symbol = db_1.Column.ofArray({ array: db_1.Column.mapToArray(atoms.number, function (n) { return (0, types_1.getElementFromAtomicNumber)(n); }), schema: db_1.Column.Schema.Aliased(db_1.Column.Schema.str) });
seq_id = db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.int);
atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
auth_asym_id: A,
auth_atom_id: type_symbol,
auth_comp_id: MOL,
auth_seq_id: seq_id,
Cartn_x: db_1.Column.asArrayColumn(atoms.x, Float32Array),
Cartn_y: db_1.Column.asArrayColumn(atoms.y, Float32Array),
Cartn_z: db_1.Column.asArrayColumn(atoms.z, Float32Array),
id: db_1.Column.range(0, atoms.count - 1),
label_asym_id: A,
label_atom_id: type_symbol,
label_comp_id: MOL,
label_seq_id: seq_id,
label_entity_id: db_1.Column.ofConst('1', atoms.count, db_1.Column.Schema.str),
occupancy: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.float),
type_symbol: type_symbol,
pdbx_PDB_model_num: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.int),
}, atoms.count);
entityBuilder = new entity_1.EntityBuilder();
entityBuilder.setNames([['MOL', 'Unknown Entity']]);
entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
componentBuilder.add('MOL', 0);
basics = (0, schema_1.createBasic)({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site: atom_site
});
return [4 /*yield*/, (0, parser_1.createModels)(basics, MolFormat.create(cube), ctx)];
case 1: return [2 /*return*/, _a.sent()];
}
});
});
}
var MolFormat;
(function (MolFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'cube';
}
MolFormat.is = is;
function create(cube) {
return { kind: 'cube', name: cube.header.comment1, data: cube };
}
MolFormat.create = create;
})(MolFormat || (MolFormat = {}));
function trajectoryFromCube(cube) {
return mol_task_1.Task.create('Parse Cube', function (ctx) { return getModels(cube, ctx); });
}
exports.trajectoryFromCube = trajectoryFromCube;
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