molstar/lib/mol-model-formats/structure/xyz.js

A comprehensive macromolecular library.

/**
 * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 */
import { Column, Table } from '../../mol-data/db';
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(mol, ctx) {
    var molecules = mol.molecules;
    var count = 0;
    for (var _i = 0, molecules_1 = molecules; _i < molecules_1.length; _i++) {
        var m = molecules_1[_i];
        count += m.count;
    }
    var type_symbols = new Array(count);
    var id = new Int32Array(count);
    var x = new Float32Array(count);
    var y = new Float32Array(count);
    var z = new Float32Array(count);
    var model_num = new Int32Array(count);
    var offset = 0;
    for (var i = 0; i < molecules.length; i++) {
        var m = molecules[i];
        for (var j = 0; j < m.count; j++) {
            type_symbols[offset] = m.type_symbol.value(j);
            x[offset] = m.x.value(j);
            y[offset] = m.y.value(j);
            z[offset] = m.z.value(j);
            id[offset] = j;
            model_num[offset] = i;
            offset++;
        }
    }
    var MOL = Column.ofConst('MOL', count, Column.Schema.str);
    var A = Column.ofConst('A', count, Column.Schema.str);
    var seq_id = Column.ofConst(1, count, Column.Schema.int);
    var type_symbol = Column.ofStringArray(type_symbols);
    var 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.ofFloatArray(x),
        Cartn_y: Column.ofFloatArray(y),
        Cartn_z: Column.ofFloatArray(z),
        id: Column.ofIntArray(id),
        label_asym_id: A,
        label_atom_id: type_symbol,
        label_comp_id: MOL,
        label_seq_id: seq_id,
        label_entity_id: Column.ofConst('1', count, Column.Schema.str),
        occupancy: Column.ofConst(1, count, Column.Schema.float),
        type_symbol: type_symbol,
        pdbx_PDB_model_num: Column.ofIntArray(model_num),
    }, count);
    var entityBuilder = new EntityBuilder();
    entityBuilder.setNames([['MOL', 'Unknown Entity']]);
    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
    var componentBuilder = new ComponentBuilder(seq_id, type_symbol);
    componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
    componentBuilder.add('MOL', 0);
    var basic = createBasic({
        entity: entityBuilder.getEntityTable(),
        chem_comp: componentBuilder.getChemCompTable(),
        atom_site: atom_site
    });
    return createModels(basic, XyzFormat.create(mol), ctx);
}
//
export { XyzFormat };
var XyzFormat;
(function (XyzFormat) {
    function is(x) {
        return (x === null || x === void 0 ? void 0 : x.kind) === 'xyz';
    }
    XyzFormat.is = is;
    function create(mol) {
        return { kind: 'xyz', name: 'xyz', data: mol };
    }
    XyzFormat.create = create;
})(XyzFormat || (XyzFormat = {}));
export function trajectoryFromXyz(mol) {
    return Task.create('Parse XYZ', function (ctx) { return getModels(mol, ctx); });
}