molstar
Version:
A comprehensive macromolecular library.
74 lines (73 loc) • 3.88 kB
JavaScript
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { __awaiter, __generator } from "tslib";
import { Column, Table } from '../../mol-data/db';
import { getElementFromAtomicNumber } from '../../mol-model/structure/model/types';
import { Task } from '../../mol-task';
import { createModels } from './basic/parser';
import { BasicSchema, createBasic } from './basic/schema';
import { ComponentBuilder } from './common/component';
import { EntityBuilder } from './common/entity';
function getModels(cube, ctx) {
return __awaiter(this, void 0, void 0, function () {
var atoms, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basic;
return __generator(this, function (_a) {
switch (_a.label) {
case 0:
atoms = cube.atoms;
MOL = Column.ofConst('MOL', cube.atoms.count, Column.Schema.str);
A = Column.ofConst('A', cube.atoms.count, Column.Schema.str);
type_symbol = Column.ofArray({ array: Column.mapToArray(atoms.number, function (n) { return getElementFromAtomicNumber(n); }), schema: Column.Schema.Aliased(Column.Schema.str) });
seq_id = Column.ofConst(1, atoms.count, Column.Schema.int);
atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
auth_asym_id: A,
auth_atom_id: type_symbol,
auth_comp_id: MOL,
auth_seq_id: seq_id,
Cartn_x: Column.asArrayColumn(atoms.x, Float32Array),
Cartn_y: Column.asArrayColumn(atoms.y, Float32Array),
Cartn_z: Column.asArrayColumn(atoms.z, Float32Array),
id: 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: Column.ofConst('1', atoms.count, Column.Schema.str),
occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
type_symbol: type_symbol,
pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
}, atoms.count);
entityBuilder = new EntityBuilder();
entityBuilder.setNames([['MOL', 'Unknown Entity']]);
entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
componentBuilder = new ComponentBuilder(seq_id, type_symbol);
componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
componentBuilder.add('MOL', 0);
basic = createBasic({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site: atom_site
});
return [4 /*yield*/, createModels(basic, 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 = {}));
export function trajectoryFromCube(cube) {
return Task.create('Parse Cube', function (ctx) { return getModels(cube, ctx); });
}