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- /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
- import { parsePsf } from '../psf/parser';
- const psfString = `PSF CMAP CHEQ
- 2 !NTITLE
- * BETA HARPIN IN IMPLICIT SOLVENT
- * DATE: 11/22/10 16:54: 9 CREATED BY USER: aokur
- 42 !NATOM
- 1 ALA3 1 ALA CAY 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
- 2 ALA3 1 ALA HY1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 3 ALA3 1 ALA HY2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 4 ALA3 1 ALA HY3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 5 ALA3 1 ALA CY 20 0.510000 12.0110 0 0.00000 -0.301140E-02
- 6 ALA3 1 ALA OY 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
- 7 ALA3 1 ALA N 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
- 8 ALA3 1 ALA HN 1 0.310000 1.00800 0 0.00000 -0.301140E-02
- 9 ALA3 1 ALA CA 22 0.700000E-01 12.0110 0 0.00000 -0.301140E-02
- 10 ALA3 1 ALA HA 6 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 11 ALA3 1 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
- 12 ALA3 1 ALA HB1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 13 ALA3 1 ALA HB2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 14 ALA3 1 ALA HB3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 15 ALA3 1 ALA C 20 0.510000 12.0110 0 0.00000 -0.301140E-02
- 16 ALA3 1 ALA O 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
- 17 ALA3 2 ALA N 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
- 18 ALA3 2 ALA HN 1 0.310000 1.00800 0 0.00000 -0.301140E-02
- 19 ALA3 2 ALA CA 22 0.700000E-01 12.0110 0 0.00000 -0.301140E-02
- 20 ALA3 2 ALA HA 6 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 21 ALA3 2 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
- 22 ALA3 2 ALA HB1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 23 ALA3 2 ALA HB2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 24 ALA3 2 ALA HB3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 25 ALA3 2 ALA C 20 0.510000 12.0110 0 0.00000 -0.301140E-02
- 26 ALA3 2 ALA O 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
- 27 ALA3 3 ALA N 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
- 28 ALA3 3 ALA HN 1 0.310000 1.00800 0 0.00000 -0.301140E-02
- 29 ALA3 3 ALA CA 22 0.700000E-01 12.0110 0 0.00000 -0.301140E-02
- 30 ALA3 3 ALA HA 6 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 31 ALA3 3 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
- 32 ALA3 3 ALA HB1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 33 ALA3 3 ALA HB2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 34 ALA3 3 ALA HB3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 35 ALA3 3 ALA C 20 0.510000 12.0110 0 0.00000 -0.301140E-02
- 36 ALA3 3 ALA O 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
- 37 ALA3 3 ALA NT 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
- 38 ALA3 3 ALA HNT 1 0.310000 1.00800 0 0.00000 -0.301140E-02
- 39 ALA3 3 ALA CAT 24 -0.110000 12.0110 0 0.00000 -0.301140E-02
- 40 ALA3 3 ALA HT1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 41 ALA3 3 ALA HT2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 42 ALA3 3 ALA HT3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
- 41 !NBOND: bonds
- 5 1 5 7 1 2 1 3
- 1 4 6 5 11 9 7 8
- 7 9 15 9 15 17 9 10
- 11 12 11 13 11 14 16 15
- 21 19 17 18 17 19 25 19
- 25 27 19 20 21 22 21 23
- 21 24 26 25 31 29 27 28
- 27 29 35 29 29 30 31 32
- 31 33 31 34 36 35 35 37
- 37 38 37 39 39 40 39 41
- 39 42
- `
- describe('psf reader', () => {
- it('basic', async () => {
- const parsed = await parsePsf(psfString).run();
- if (parsed.isError) {
- throw new Error(parsed.message)
- }
- const psfFile = parsed.result;
- const { id, title, atoms, bonds } = psfFile;
- expect(id).toBe('PSF CMAP CHEQ')
- expect(title).toEqual([
- 'BETA HARPIN IN IMPLICIT SOLVENT',
- 'DATE: 11/22/10 16:54: 9 CREATED BY USER: aokur'
- ])
- expect(atoms.atomId.value(0)).toBe(1)
- expect(atoms.atomId.value(41)).toBe(42)
- expect(atoms.segmentName.value(0)).toBe('ALA3')
- expect(atoms.residueId.value(0)).toBe(1)
- expect(atoms.residueId.value(41)).toBe(3)
- expect(atoms.residueName.value(0)).toBe('ALA')
- expect(atoms.atomName.value(0)).toBe('CAY')
- expect(atoms.atomName.value(41)).toBe('HT3')
- expect(atoms.atomType.value(0)).toBe('24')
- expect(atoms.atomType.value(41)).toBe('3')
- expect(atoms.charge.value(0)).toBeCloseTo(-0.270000, 0.00001)
- expect(atoms.charge.value(41)).toBeCloseTo(0.090000, 0.00001)
- expect(atoms.mass.value(0)).toBeCloseTo(12.0110, 0.00001)
- expect(atoms.mass.value(41)).toBeCloseTo(1.00800, 0.00001)
- expect(bonds.atomIdA.value(0)).toBe(5)
- expect(bonds.atomIdB.value(0)).toBe(1)
- expect(bonds.atomIdA.value(40)).toBe(39)
- expect(bonds.atomIdB.value(40)).toBe(42)
- });
- });
|
