molstar
Version:
A comprehensive macromolecular library.
90 lines (89 loc) • 3.55 kB
JavaScript
"use strict";
/**
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.XyzFormat = void 0;
exports.trajectoryFromXyz = trajectoryFromXyz;
const db_1 = require("../../mol-data/db");
const types_1 = require("../../mol-model/structure/model/types");
const mol_task_1 = require("../../mol-task");
const parser_1 = require("./basic/parser");
const schema_1 = require("./basic/schema");
const component_1 = require("./common/component");
const entity_1 = require("./common/entity");
function getModels(mol, ctx) {
const { molecules } = mol;
let count = 0;
for (const m of molecules)
count += m.count;
const type_symbols = new Array(count);
const id = new Int32Array(count);
const x = new Float32Array(count);
const y = new Float32Array(count);
const z = new Float32Array(count);
const model_num = new Int32Array(count);
let offset = 0;
for (let i = 0; i < molecules.length; i++) {
const m = molecules[i];
for (let 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++;
}
}
const MOL = db_1.Column.ofConst('MOL', count, db_1.Column.Schema.str);
const A = db_1.Column.ofConst('A', count, 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_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.ofFloatArray(x),
Cartn_y: db_1.Column.ofFloatArray(y),
Cartn_z: db_1.Column.ofFloatArray(z),
id: db_1.Column.ofIntArray(id),
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', 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_1.createBasic)({
entity: entityBuilder.getEntityTable(),
chem_comp: componentBuilder.getChemCompTable(),
atom_site
});
return (0, parser_1.createModels)(basic, XyzFormat.create(mol), ctx);
}
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 || (exports.XyzFormat = XyzFormat = {}));
function trajectoryFromXyz(mol) {
return mol_task_1.Task.create('Parse XYZ', ctx => getModels(mol, ctx));
}