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

A comprehensive macromolecular library.

/**
 * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
import { Task } from '../../mol-task';
import { Coordinates, Time } from '../../mol-model/structure/coordinates';
import { Cell } from '../../mol-math/geometry/spacegroup/cell';
import { Vec3 } from '../../mol-math/linear-algebra';
export function coordinatesFromTrr(file) {
    return Task.create('Parse TRR', async (ctx) => {
        await ctx.update('Converting to coordinates');
        const deltaTime = Time(file.deltaTime, 'step');
        const offsetTime = Time(file.timeOffset, deltaTime.unit);
        const frames = [];
        for (let i = 0, il = file.frames.length; i < il; ++i) {
            const box = file.boxes[i];
            const x = Vec3.fromArray(Vec3(), box, 0);
            const y = Vec3.fromArray(Vec3(), box, 3);
            const z = Vec3.fromArray(Vec3(), box, 6);
            frames.push({
                elementCount: file.frames[i].count,
                cell: Cell.fromBasis(x, y, z),
                x: file.frames[i].x,
                y: file.frames[i].y,
                z: file.frames[i].z,
                xyzOrdering: { isIdentity: true },
                time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit)
            });
        }
        return Coordinates.create(frames, deltaTime, offsetTime);
    });
}