def test_json(self):
f1 = MagresFile(open(os.path.join(DATA_DIR, "ethanol", "ethanol-nmr.magres")))
json = f1.as_json()
f2 = MagresFile.load_json(json)
self.assertEqual(f1.data_dict, f2.data_dict)
class AtomsTest(unittest.TestCase):
cubic = MagresFile.load_json(
'{"atoms": {"units": [["atom", "Angstrom"], ["lattice", "Angstrom"]], "lattice": [[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]], "atom": [{"index": 1, "position": [0.0, 0.0, 0.0], "species": "H", "label": "H"}]}}'
)
orthorhombic = MagresFile.load_json(
'{"atoms": {"units": [["atom", "Angstrom"], ["lattice", "Angstrom"]], "lattice": [[[1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]]], "atom": [{"index": 1, "position": [0.0, 0.0, 0.0], "species": "H", "label": "H"}]}}'
)
species = MagresFile.load_json(
'{"atoms": {"units": [["atom", "Angstrom"], ["lattice", "Angstrom"]], "lattice": [[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]], "atom": [{"index": 1, "position": [0.0, 0.0, 0.0], "species": "H", "label": "H"},{"index": 1, "position": [0.0, 0.0, 1.0], "species": "C", "label": "C1"},{"index": 1, "position": [0.0, 0.0, 2.0], "species": "C", "label": "C2"}]}}'
)
def test_within_cubic(self):
atoms = MagresAtoms.load_magres(self.cubic)
self.assertEquals(len(atoms), 1)
p = atoms[0].position
self.assertEquals(len(atoms.within(p, 1.0)), 7)
num_within_3 = 0
for atom in atoms.within(atoms[0], 5.0):
if atom.dist(atoms[0]) <= 3.0:
num_within_3 += 1
self.assertEquals(len(atoms.within(p, 3.0)), num_within_3)
self.assertEquals(len(atoms.within(p, 5.0).within(p, 2.0)),
len(atoms.within(p, 2.0).within(p, 5.0)))
def test_within_orthorhombic(self):
atoms = MagresAtoms.load_magres(self.orthorhombic)
self.assertEquals(len(atoms), 1)
p = atoms[0].position
self.assertEquals(len(atoms.within(p, 1.0)), 3)
num_within_3 = 0
for atom in atoms.within(p, 10.0):
if atom.dist(atoms[0]) <= 3.0:
num_within_3 += 1
self.assertEquals(len(atoms.within(p, 3.0)), num_within_3)
self.assertEquals(len(atoms.within(p, 5.0).within(p, 2.0)),
len(atoms.within(p, 2.0).within(p, 5.0)))
def test_species(self):
atoms = MagresAtoms.load_magres(self.species)
self.assertEquals(len(atoms), 3)
self.assertEquals(len(atoms.species('H')), 1)
self.assertEquals(len(atoms.species('C')), 2)
def test_labels(self):
atoms = MagresAtoms.load_magres(self.species)
self.assertEquals(len(atoms), 3)
self.assertEquals(len(atoms.label('H')), 1)
self.assertEquals(len(atoms.label('C')), 0)
self.assertEquals(len(atoms.label('C1')), 1)
self.assertEquals(len(atoms.label('C2')), 1)
