molstar
Version:
A comprehensive macromolecular library.
90 lines • 5.08 kB
JavaScript
;
/**
* Copyright (c) 2019-2020 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.trajectoryFromMol = exports.MolFormat = exports.getMolModels = void 0;
var tslib_1 = require("tslib");
var db_1 = require("../../mol-data/db");
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");
var index_pair_1 = require("./property/bonds/index-pair");
function getMolModels(mol, format, ctx) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var atoms, bonds, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
atoms = mol.atoms, bonds = mol.bonds;
MOL = db_1.Column.ofConst('MOL', mol.atoms.count, db_1.Column.Schema.str);
A = db_1.Column.ofConst('A', mol.atoms.count, db_1.Column.Schema.str);
type_symbol = db_1.Column.asArrayColumn(atoms.type_symbol);
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, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
case 1:
models = _a.sent();
if (models.frameCount > 0) {
indexA = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.atomIdxA, function (x) { return x - 1; }, Int32Array));
indexB = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.atomIdxB, function (x) { return x - 1; }, Int32Array));
order = db_1.Column.asArrayColumn(bonds.order, Int32Array);
pairBonds = index_pair_1.IndexPairBonds.fromData({ pairs: { indexA: indexA, indexB: indexB, order: order }, count: atoms.count });
index_pair_1.IndexPairBonds.Provider.set(models.representative, pairBonds);
}
return [2 /*return*/, models];
}
});
});
}
exports.getMolModels = getMolModels;
var MolFormat;
(function (MolFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'mol';
}
MolFormat.is = is;
function create(mol) {
return { kind: 'mol', name: mol.title, data: mol };
}
MolFormat.create = create;
})(MolFormat || (MolFormat = {}));
exports.MolFormat = MolFormat;
function trajectoryFromMol(mol) {
return mol_task_1.Task.create('Parse MOL', function (ctx) { return getMolModels(mol, void 0, ctx); });
}
exports.trajectoryFromMol = trajectoryFromMol;
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