def test_gro_velocities(self): """ Test parsing and writing GROMACS GRO files with velocities """ gro = load_file(get_fn('1aki.ff99sbildn.gro')) self.assertIsInstance(gro, Structure) vel = np.random.rand(len(gro.atoms), 3) gro.velocities = vel fn = get_fn('test.gro', written=True) gro.save(fn) self.assertTrue(GromacsGroFile.id_format(fn)) gro.save(fn, overwrite=True, precision=8) self.assertTrue(GromacsGroFile.id_format(fn)) with open(fn) as f: tmp = GromacsGroFile.parse(f) np.testing.assert_allclose(vel, tmp.velocities, atol=1e-8)
def test_gro_detection(self): """ Tests automatic detection of GROMACS GRO files """ fn = get_fn('candidate.gro', written=True) with open(fn, 'w') as f: f.write('Some title\n 1000\n aISNot a valid format\n') self.assertFalse(GromacsGroFile.id_format(fn))