def __init__(self, filename, name=""):
"""
attempts to open the given trajectory
:param filename: the file name
:param name: the trajectory name inside the file, as given in the simulation
"""
assert _os.path.exists(
filename), "The file '{}' did not exist!".format(filename)
self._filename = filename
self._name = name
self._diffusion_constants = _io_utils.get_diffusion_constants(filename)
self._particle_types = _io_utils.get_particle_types(filename)
self._reactions = []
self._inverse_types_map = {
v: k
for k, v in self.particle_types.items()
}
self._general = GeneralInformation(filename)
for _, reaction in _io_utils.get_reactions(filename).items():
info = ReactionInfo(reaction["name"], reaction["id"],
reaction["n_educts"], reaction["n_products"],
reaction["rate"], reaction["educt_distance"],
reaction["product_distance"],
reaction["educt_types"],
reaction["product_types"],
self._inverse_types_map)
self._reactions.append(info)
def test_particle_types_info(self):
p_types = ioutils.get_particle_types(self.fname)
# assuming that type ids are in accordance to order of registration
np.testing.assert_equal(p_types["A"], 0)
np.testing.assert_equal(p_types["B"], 1)
np.testing.assert_equal(p_types["C"], 2)
diff_constants = ioutils.get_diffusion_constants(self.fname)
np.testing.assert_equal(diff_constants["A"], 1.)
np.testing.assert_equal(diff_constants["B"], 2.)
np.testing.assert_equal(diff_constants["C"], 3.)
def test_particle_types_info(self):
p_types = ioutils.get_particle_types(self.fname)
# assuming that type ids are in accordance to order of registration
np.testing.assert_equal(p_types["A"], 0)
np.testing.assert_equal(p_types["B"], 1)
np.testing.assert_equal(p_types["C"], 2)
diff_constants = ioutils.get_diffusion_constants(self.fname)
np.testing.assert_equal(diff_constants["A"], 1.)
np.testing.assert_equal(diff_constants["B"], 2.)
np.testing.assert_equal(diff_constants["C"], 3.)
def __init__(self, filename, name=""):
"""
attempts to open the given trajectory
:param filename: the file name
:param name: the trajectory name inside the file, as given in the simulation
"""
assert _os.path.exists(filename), "The file '{}' did not exist!".format(filename)
self._filename = filename
self._name = name
self._diffusion_constants = _io_utils.get_diffusion_constants(filename)
self._particle_types = _io_utils.get_particle_types(filename)
self._reactions = []
self._inverse_types_map = {v: k for k, v in self.particle_types.items()}
self._general = GeneralInformation(filename)
for _, reaction in _io_utils.get_reactions(filename).items():
info = ReactionInfo(reaction["name"], reaction["id"], reaction["n_educts"],
reaction["n_products"], reaction["rate"], reaction["educt_distance"],
reaction["product_distance"], reaction["educt_types"], reaction["product_types"],
self._inverse_types_map)
self._reactions.append(info)
