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(N_ATOMS, 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 = master_runner.MasterReplicaExchangeRunner(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 = ConstantTemperatureScaler(300.0)
store.save_system(s)
# create and store the options
o = 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_runner_equals_fake_runner_should_create_fake_runner(self):
system = mock.Mock()
comm = mock.Mock()
options = RunOptions()
options.runner = "fake_runner"
with mock.patch("meld.system.runner.FakeSystemRunner") as mock_runner:
get_runner(system, options, comm)
self.assertEqual(mock_runner.call_count, 1)
def test_runner_equals_openmm_should_create_openmm_runner(self):
system = mock.Mock()
comm = mock.Mock()
options = RunOptions()
options.runner = "openmm"
with mock.patch("meld.system.openmm_runner.runner.OpenMMRunner") as mock_runner:
get_runner(system, options, comm)
self.assertEqual(mock_runner.call_count, 1)
def test_runner_equals_fake_runner_should_create_fake_runner(self):
system = mock.Mock()
comm = mock.Mock()
options = RunOptions()
options.runner = 'fake_runner'
with mock.patch('meld.system.runner.FakeSystemRunner') as mock_runner:
get_runner(system, options, comm)
self.assertEqual(mock_runner.call_count, 1)
def test_runner_equals_openmm_should_create_openmm_runner(self):
system = mock.Mock()
comm = mock.Mock()
options = RunOptions()
options.runner = 'openmm'
with mock.patch('meld.system.runner.OpenMMRunner') as mock_runner:
get_runner(system, options, comm)
self.assertEqual(mock_runner.call_count, 1)
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(N_ATOMS,
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 = master_runner.MasterReplicaExchangeRunner(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 = ConstantTemperatureScaler(300.)
store.save_system(s)
# create and store the options
o = 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_raises_when_system_has_no_temperature_scaler(self):
self.system.temperature_scaler = None
with self.assertRaises(RuntimeError):
OpenMMRunner(self.system, RunOptions())
def setUp(self):
self.options = RunOptions()
def setUp(self):
self.options = RunOptions(solvation="explicit")