TmMolStar/src/mol-model-formats/structure/trr.ts

/**
 * 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 { TrrFile } from '../../mol-io/reader/trr/parser';
import { Coordinates, Frame, 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: TrrFile): Task<Coordinates> {
    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: Frame[] = [];
        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);
    });
}