molstar
Version:
A comprehensive macromolecular library.
90 lines (89 loc) • 4.13 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>
* @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
*/
import { Column, Table } from '../../mol-data/db';
import { formalChargeMapper } from '../../mol-io/reader/mol/parser';
import { MoleculeType } 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';
import { IndexPairBonds } from './property/bonds/index-pair';
export async function getMolModels(mol, format, ctx) {
const { atoms, bonds, formalCharges } = mol;
const MOL = Column.ofConst('MOL', mol.atoms.count, Column.Schema.str);
const A = Column.ofConst('A', mol.atoms.count, Column.Schema.str);
const type_symbol = Column.asArrayColumn(atoms.type_symbol);
const seq_id = Column.ofConst(1, atoms.count, Column.Schema.int);
const computedFormalCharges = new Int32Array(mol.atoms.count);
if (formalCharges.atomIdx.rowCount > 0) {
for (let i = 0; i < formalCharges.atomIdx.rowCount; i++) {
computedFormalCharges[formalCharges.atomIdx.value(i) - 1] = formalCharges.charge.value(i);
}
}
else {
for (let i = 0; i < mol.atoms.count; i++) {
computedFormalCharges[i] = formalChargeMapper(atoms.formal_charge.value(i));
}
}
const 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(1, atoms.count),
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,
pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
pdbx_formal_charge: Column.ofIntArray(computedFormalCharges)
}, atoms.count);
const entityBuilder = new EntityBuilder();
entityBuilder.setNames([['MOL', 'Unknown Entity']]);
entityBuilder.getEntityId('MOL', MoleculeType.Unknown, 'A');
const componentBuilder = new ComponentBuilder(seq_id, type_symbol);
componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
componentBuilder.add('MOL', 0);
const basic = createBasic({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site
});
const models = await createModels(basic, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx);
if (models.frameCount > 0) {
const indexA = Column.ofIntArray(Column.mapToArray(bonds.atomIdxA, x => x - 1, Int32Array));
const indexB = Column.ofIntArray(Column.mapToArray(bonds.atomIdxB, x => x - 1, Int32Array));
const order = Column.asArrayColumn(bonds.order, Int32Array);
const pairBonds = IndexPairBonds.fromData({ pairs: { indexA, indexB, order }, count: atoms.count }, { maxDistance: Infinity });
IndexPairBonds.Provider.set(models.representative, pairBonds);
}
return models;
}
//
export { MolFormat };
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 = {}));
export function trajectoryFromMol(mol) {
return Task.create('Parse MOL', ctx => getMolModels(mol, void 0, ctx));
}