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 testReadWriteHighPrecisionGroFile(self): """ Tests reading/writing high-precision GRO files """ gro = GromacsGroFile.parse(get_fn('1aki.ff99sbildn.gro')) GromacsGroFile.write(gro, get_fn('1aki.ff99sbildn_highprec.gro', written=True), precision=6) self.assertTrue(diff_files(get_saved_fn('1aki.ff99sbildn_highprec.gro'), get_fn('1aki.ff99sbildn_highprec.gro', written=True) ) ) gro2 = GromacsGroFile.parse(get_fn('1aki.ff99sbildn_highprec.gro', written=True)) gro3 = load_file(get_fn('1aki.ff99sbildn_highprec.gro', written=True)) self.assertIsInstance(gro3, Structure) for a1, a2, a3 in zip(gro.atoms, gro2.atoms, gro3.atoms): self.assertEqual(a1.name, a2.name) self.assertEqual(a3.name, a2.name) self.assertEqual(a1.xx, a2.xx) self.assertEqual(a3.xx, a2.xx) self.assertEqual(a1.xy, a2.xy) self.assertEqual(a3.xy, a2.xy) self.assertEqual(a1.xz, a2.xz) self.assertEqual(a3.xz, a2.xz)
def testWriteGroFile(self): """ Tests writing GRO file """ gro = GromacsGroFile.parse(get_fn('1aki.ff99sbildn.gro')) GromacsGroFile.write(gro, get_fn('1aki.ff99sbildn.gro', written=True)) gro = load_file(get_fn('1aki.ff99sbildn.gro', written=True)) self.assertIsInstance(gro, Structure) self.assertEqual(len(gro.atoms), 1960) self.assertEqual(len(gro.residues), 129) self.assertAlmostEqual(gro.atoms[0].xx, 44.6) self.assertAlmostEqual(gro.atoms[0].xy, 49.86) self.assertAlmostEqual(gro.atoms[0].xz, 18.10) self.assertAlmostEqual(gro.atoms[1959].xx, 50.97) self.assertAlmostEqual(gro.atoms[1959].xy, 39.80) self.assertAlmostEqual(gro.atoms[1959].xz, 38.64) self.assertAlmostEqual(gro.box[0], 74.1008) self.assertAlmostEqual(gro.box[1], 74.10080712) self.assertAlmostEqual(gro.box[2], 74.10074585) self.assertAlmostEqual(gro.box[3], 70.52882666) self.assertAlmostEqual(gro.box[4], 109.47126278) self.assertAlmostEqual(gro.box[5], 70.52875398)
def testReadGroFile(self): """ Tests reading GRO file """ gro = GromacsGroFile.parse(get_fn('1aki.ff99sbildn.gro')) self.assertIsInstance(gro, Structure) self.assertEqual(len(gro.atoms), 1960) self.assertEqual(len(gro.residues), 129) self.assertAlmostEqual(gro.atoms[0].xx, 44.6) self.assertAlmostEqual(gro.atoms[0].xy, 49.86) self.assertAlmostEqual(gro.atoms[0].xz, 18.10) self.assertAlmostEqual(gro.atoms[1959].xx, 50.97) self.assertAlmostEqual(gro.atoms[1959].xy, 39.80) self.assertAlmostEqual(gro.atoms[1959].xz, 38.64) self.assertAlmostEqual(gro.box[0], 74.1008) self.assertAlmostEqual(gro.box[1], 74.10080712) self.assertAlmostEqual(gro.box[2], 74.10074585) self.assertAlmostEqual(gro.box[3], 70.52882666) self.assertAlmostEqual(gro.box[4], 109.47126278) self.assertAlmostEqual(gro.box[5], 70.52875398) # Check atomic number and mass assignment self.assertEqual(gro.atoms[0].atomic_number, 7) self.assertEqual(gro.atoms[0].mass, 14.0067)
def __init__(self, inputs: dict, working_dir: str = None): super().__init__(inputs, working_dir) self.grompp_cmd = inputs["grompp_cmd"].split() self.mdp = MDPHandler(inputs["mdp_file"]) self.gro_struct = GromacsGroFile.parse(inputs["gro_file"], skip_bonds=True) # This is a hacky way of getting around parmed's Structure. Structure # implements a correct deep copy in __copy__, but does not implement # __deepcopy__, and the default behavior is incorrect. Since # GromacsEngine gets deep copied, we need the correct version to be called. # See https://github.com/ParmEd/ParmEd/issues/1205 for if this can be # safely removed self.gro_struct.__deepcopy__ = lambda memo_dict: self.gro_struct.__copy__() with open(inputs["top_file"], "r") as file: self.topology = file.read() self.set_delta_t(inputs["delta_t"]) self.should_pin = inputs["should_pin"]