TmMolStar/src/reader/spec/gro.spec.ts

/*
 * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @author David Sehnal <david.sehnal@gmail.com>
 */

import Gro from '../gro/index'

const groString = `MD of 2 waters, t= 4.2
    6
    1WATER  OW1    1   0.126   1.624   1.679  0.1227 -0.0580  0.0434
    1WATER  HW2    2   0.190   1.661   1.747  0.8085  0.3191 -0.7791
    1WATER  HW3    3   0.177   1.568   1.613 -0.9045 -2.6469  1.3180
    2WATER  OW1    4   1.275   0.053   0.622  0.2519  0.3140 -0.1734
    2WATER  HW2    5   1.337   0.002   0.680 -1.0641 -1.1349  0.0257
    2WATER  HW3    6   1.326   0.120   0.568  1.9427 -0.8216 -0.0244
   1.82060   1.82060   1.82060`

const groStringHighPrecision = `Generated by trjconv : 2168 system t=  15.00000
    3
    1ETH     C1    1   2.735383   2.672010   1.450194  0.2345 -0.1622 0.2097
    1ETH    H11    2   0.015804   2.716597   1.460588  0.8528 -0.7984 0.6605
    1ETH    H12    3   2.744822   2.565544   1.409227 -2.3812  2.8618 1.8101
   1.82060   1.82060   1.82060`

describe('gro reader', () => {
    it('basic', () => {
        const parsed = Gro.parse(groString)

        if (parsed.isError) {
            console.log(parsed)
        } else {
            const groFile = parsed.result;
            const data = Gro.schema(groFile.blocks[0]);

            const { header, atoms } = data;
            if (header._isDefined) {
                expect(header.title.value(0)).toBe('MD of 2 waters')
                expect(header.timeInPs.value(0)).toBeCloseTo(4.2)
                expect(header.numberOfAtoms.value(0)).toBe(6)

                expect(header.boxX.value(0)).toBeCloseTo(1.82060)
                expect(header.boxY.value(0)).toBeCloseTo(1.82060)
                expect(header.boxZ.value(0)).toBeCloseTo(1.82060)
            } else {
                console.error('no header')
            }

            if (atoms._rowCount === 6)  {
                expect(atoms.x.value(0)).toBeCloseTo(0.126);
                expect(atoms.y.value(0)).toBeCloseTo(1.624);
                expect(atoms.z.value(0)).toBeCloseTo(1.679);

                // TODO: check velocities when they are parsed.
            } else {
                console.error('no atoms');
            }
        }
    })

    it('high precision', () => {
        const parsed = Gro.parse(groStringHighPrecision)

        if (parsed.isError) {
            console.log(parsed)
        } else {
            const groFile = parsed.result;
            const data = Gro.schema(groFile.blocks[0]);

            const { header, atoms } = data;
            if (header._isDefined) {
                expect(header.title.value(0)).toBe('Generated by trjconv : 2168 system')
                expect(header.timeInPs.value(0)).toBeCloseTo(15)
                expect(header.numberOfAtoms.value(0)).toBe(3)

                expect(header.boxX.value(0)).toBeCloseTo(1.82060)
                expect(header.boxY.value(0)).toBeCloseTo(1.82060)
                expect(header.boxZ.value(0)).toBeCloseTo(1.82060)
            } else {
                console.error('no header')
            }

            if (atoms._rowCount === 3)  {
                // TODO: test when high-prec parser is available
                // expect(atoms.x.value(1)).toBeCloseTo(0.015804, 0.00001);
                // expect(atoms.y.value(1)).toBeCloseTo(2.716597, 0.00001);
                // expect(atoms.z.value(1)).toBeCloseTo(1.460588, 0.00001);

                // TODO: check velocities when they are parsed.
            } else {
                console.error('no atoms');
            }
        }
    })
});