def get_pdb_writer(self) -> pdb_writer.PDBWriter:
"""
Get the PDBWriter
"""
return pdb_writer.PDBWriter(
list(range(1, len(self._atom_names) + 1)),
self._atom_names,
self._residue_numbers,
self._residue_names,
)
def setUp(self):
self.atom_numbers = [1000, 1001]
self.atom_names = ["ABCD", "A2"]
self.residue_numbers = [999, 1000]
self.residue_names = ["XYZ", "R2"]
self.coords = np.zeros((2, 3))
self.coords[0, :] = 0.1
self.coords[1, :] = 0.2
self.writer = pdb_writer.PDBWriter(self.atom_numbers, self.atom_names,
self.residue_numbers,
self.residue_names)
def setup_system():
# create a store
writer = pdb_writer.PDBWriter(
range(N_ATOMS), ["CA"] * N_ATOMS, [1] * N_ATOMS, ["ALA"] * N_ATOMS
)
store = vault.DataStore(gen_state(0), N_REPLICAS, writer, block_size=BACKUP_FREQ)
store.initialize(mode="w")
# create and store the remd_runner
l = ladder.NearestNeighborLadder(n_trials=100)
policy = adaptor.AdaptationPolicy(1.0, 50, 100)
a = adaptor.EqualAcceptanceAdaptor(n_replicas=N_REPLICAS, adaptation_policy=policy)
remd_runner = leader.LeaderReplicaExchangeRunner(
N_REPLICAS, max_steps=N_STEPS, ladder=l, adaptor=a
)
store.save_remd_runner(remd_runner)
# create and store the communicator
c = comm.MPICommunicator(N_ATOMS, N_REPLICAS)
store.save_communicator(c)
# create and store the fake system
s = helper.FakeSystem()
s.temperature_scaler = temperature.ConstantTemperatureScaler(300.0)
store.save_system(s)
# create and store the options
o = options.RunOptions()
o.runner = "fake_runner"
store.save_run_options(o)
# create and save the initial states
states = [gen_state(i) for i in range(N_REPLICAS)]
store.save_states(states, 0)
# save data_store
store.save_data_store()
def test_should_raise_with_wrong_number_of_residue_names(self):
with self.assertRaises(AssertionError):
pdb_writer.PDBWriter(self.atom_numbers, self.atom_names,
self.residue_numbers, ["R1"])