molstar
Version:
A comprehensive macromolecular library.
158 lines (157 loc) • 7.28 kB
JavaScript
"use strict";
/**
* Copyright (c) 2024 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 Ludovic Autin <ludovic.autin@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.LammpsTrajectoryFormat = void 0;
exports.coordinatesFromLammpsTrajectory = coordinatesFromLammpsTrajectory;
exports.trajectoryFromLammpsTrajectory = trajectoryFromLammpsTrajectory;
const coordinates_1 = require("../../mol-model/structure/coordinates");
const schema_1 = require("../../mol-io/reader/lammps/schema");
const model_1 = require("../../mol-model/structure/model");
const mol_task_1 = require("../../mol-task");
const db_1 = require("../../mol-data/db");
const schema_2 = require("./basic/schema");
const component_1 = require("./common/component");
const entity_1 = require("./common/entity");
const parser_1 = require("./basic/parser");
const types_1 = require("../../mol-model/structure/model/types");
function coordinatesFromLammpsTrajectory(file, unitsStyle = 'real') {
return mol_task_1.Task.create('Parse Lammps Trajectory', async (ctx) => {
await ctx.update('Converting to coordinates');
const scale = schema_1.lammpsUnitStyles[unitsStyle].scale;
const deltaTime = (0, coordinates_1.Time)(file.deltaTime, 'step');
const offsetTime = (0, coordinates_1.Time)(file.timeOffset, deltaTime.unit);
const offset_pos = { x: 0.0, y: 0.0, z: 0.0 };
const offset_scale = { x: 1.0, y: 1.0, z: 1.0 };
const atomsMode = file.frames[0].atomMode;
const isScaled = atomsMode.includes('s');
const frames = [];
for (let i = 0, il = file.frames.length; i < il; ++i) {
const box = file.bounds[i];
if (isScaled) {
offset_scale.x = box.length[0];
offset_scale.y = box.length[1];
offset_scale.z = box.length[2];
offset_pos.x = box.lower[0];
offset_pos.y = box.lower[1];
offset_pos.z = box.lower[2];
}
const count = file.frames[i].count;
const cx = new Float32Array(count);
const cy = new Float32Array(count);
const cz = new Float32Array(count);
let offset = 0;
for (let j = 0; j < count; j++) {
cx[offset] = (file.frames[i].x.value(j) * offset_scale.x + offset_pos.x) * scale;
cy[offset] = (file.frames[i].y.value(j) * offset_scale.y + offset_pos.y) * scale;
cz[offset] = (file.frames[i].z.value(j) * offset_scale.z + offset_pos.z) * scale;
offset++;
}
frames.push({
elementCount: file.frames[i].count,
x: cx,
y: cy,
z: cz,
xyzOrdering: { isIdentity: true },
time: (0, coordinates_1.Time)(offsetTime.value + deltaTime.value * i, deltaTime.unit)
});
}
return coordinates_1.Coordinates.create(frames, deltaTime, offsetTime);
});
}
async function getModels(mol, ctx, unitsStyle = 'real') {
const atoms = mol.frames[0];
const count = atoms.count;
const atomsMode = atoms.atomMode;
const box = mol.bounds[0];
const offset_pos = { x: 0.0, y: 0.0, z: 0.0 };
const offset_scale = { x: 1.0, y: 1.0, z: 1.0 };
const scale = schema_1.lammpsUnitStyles[unitsStyle].scale;
// if caracter s in atomsMode, we need to scale the coordinates
if (atomsMode.includes('s')) {
offset_scale.x = box.length[0];
offset_scale.y = box.length[1];
offset_scale.z = box.length[2];
offset_pos.x = box.lower[0];
offset_pos.y = box.lower[1];
offset_pos.z = box.lower[2];
}
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) * offset_scale.x + offset_pos.x) * scale;
cy[offset] = (atoms.y.value(j) * offset_scale.y + offset_pos.y) * scale;
cz[offset] = (atoms.z.value(j) * offset_scale.z + offset_pos.z) * scale;
id[offset] = atoms.atomId.value(j);
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, LammpsTrajectoryFormat.create(mol), ctx);
const first = _models.representative;
const coordinates = await coordinatesFromLammpsTrajectory(mol, unitsStyle).runInContext(ctx);
return model_1.Model.trajectoryFromModelAndCoordinates(first, coordinates);
}
var LammpsTrajectoryFormat;
(function (LammpsTrajectoryFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'lammpstrj';
}
LammpsTrajectoryFormat.is = is;
function create(mol) {
return { kind: 'lammpstrj', name: 'lammpstrj', data: mol };
}
LammpsTrajectoryFormat.create = create;
})(LammpsTrajectoryFormat || (exports.LammpsTrajectoryFormat = LammpsTrajectoryFormat = {}));
function trajectoryFromLammpsTrajectory(mol, unitsStyle) {
if (unitsStyle === void 0)
unitsStyle = 'real';
return mol_task_1.Task.create('Parse Lammps Traj Data', ctx => getModels(mol, ctx, unitsStyle));
}