molstar
Version:
A comprehensive macromolecular library.
117 lines (116 loc) • 5.3 kB
JavaScript
"use strict";
/**
* Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
* @author Ludovic Autin <ludovic.autin@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.LammpsDataFormat = void 0;
exports.trajectoryFromLammpsData = trajectoryFromLammpsData;
const db_1 = require("../../mol-data/db");
const schema_1 = require("../../mol-io/reader/lammps/schema");
const structure_1 = require("../../mol-model/structure");
const types_1 = require("../../mol-model/structure/model/types");
const mol_task_1 = require("../../mol-task");
const parser_1 = require("./basic/parser");
const schema_2 = require("./basic/schema");
const component_1 = require("./common/component");
const entity_1 = require("./common/entity");
const index_pair_1 = require("./property/bonds/index-pair");
const partial_charge_1 = require("./property/partial-charge");
async function getModels(mol, ctx, unitsStyle = 'real') {
const { atoms, bonds } = mol;
const models = [];
const count = atoms.count;
const scale = schema_1.lammpsUnitStyles[unitsStyle].scale;
const type_symbols = new Array(count);
const id = new Int32Array(count);
const cx = new Float32Array(count);
const cy = new Float32Array(count);
const cz = new Float32Array(count);
const model_num = new Int32Array(count);
let offset = 0;
for (let j = 0; j < count; j++) {
type_symbols[offset] = atoms.atomType.value(j).toString();
cx[offset] = atoms.x.value(j) * scale;
cy[offset] = atoms.y.value(j) * scale;
cz[offset] = atoms.z.value(j) * scale;
id[offset] = atoms.atomId.value(j) - 1;
model_num[offset] = 0;
offset++;
}
const MOL = db_1.Column.ofConst('MOL', count, db_1.Column.Schema.str);
const asym_id = db_1.Column.ofLambda({
value: (row) => atoms.moleculeId.value(row).toString(),
rowCount: count,
schema: db_1.Column.Schema.str,
});
const seq_id = db_1.Column.ofConst(1, count, db_1.Column.Schema.int);
const type_symbol = db_1.Column.ofStringArray(type_symbols);
const atom_site = db_1.Table.ofPartialColumns(schema_2.BasicSchema.atom_site, {
auth_asym_id: asym_id,
auth_atom_id: type_symbol,
auth_comp_id: MOL,
auth_seq_id: seq_id,
Cartn_x: db_1.Column.ofFloatArray(cx),
Cartn_y: db_1.Column.ofFloatArray(cy),
Cartn_z: db_1.Column.ofFloatArray(cz),
id: db_1.Column.ofIntArray(id),
label_asym_id: asym_id,
label_atom_id: type_symbol,
label_comp_id: MOL,
label_seq_id: seq_id,
label_entity_id: db_1.Column.ofConst('1', count, db_1.Column.Schema.str),
occupancy: db_1.Column.ofConst(1, count, db_1.Column.Schema.float),
type_symbol,
pdbx_PDB_model_num: db_1.Column.ofIntArray(model_num),
}, count);
const entityBuilder = new entity_1.EntityBuilder();
entityBuilder.setNames([['MOL', 'Unknown Entity']]);
entityBuilder.getEntityId('MOL', types_1.MoleculeType.Unknown, 'A');
const componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
componentBuilder.add('MOL', 0);
const basic = (0, schema_2.createBasic)({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site
});
const _models = await (0, parser_1.createModels)(basic, LammpsDataFormat.create(mol), ctx);
if (_models.frameCount > 0) {
const first = _models.representative;
if (bonds.count !== 0) {
const indexA = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.atomIdA, x => x - 1, Int32Array));
const indexB = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.atomIdB, x => x - 1, Int32Array));
const key = bonds.bondId;
const order = db_1.Column.ofConst(1, bonds.count, db_1.Column.Schema.int);
const flag = db_1.Column.ofConst(types_1.BondType.Flag.Covalent, bonds.count, db_1.Column.Schema.int);
const pairBonds = index_pair_1.IndexPairBonds.fromData({ pairs: { key, indexA, indexB, order, flag }, count: atoms.count }, { maxDistance: Infinity });
index_pair_1.IndexPairBonds.Provider.set(first, pairBonds);
}
partial_charge_1.AtomPartialCharge.Provider.set(first, {
data: atoms.charge,
type: 'NO_CHARGES'
});
models.push(first);
}
return new structure_1.ArrayTrajectory(models);
}
var LammpsDataFormat;
(function (LammpsDataFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'data';
}
LammpsDataFormat.is = is;
function create(mol) {
return { kind: 'data', name: 'data', data: mol };
}
LammpsDataFormat.create = create;
})(LammpsDataFormat || (exports.LammpsDataFormat = LammpsDataFormat = {}));
function trajectoryFromLammpsData(mol, unitsStyle) {
if (unitsStyle === void 0)
unitsStyle = 'real';
return mol_task_1.Task.create('Parse Lammps Data', ctx => getModels(mol, ctx, unitsStyle));
}