def __init__(self, engine):
descriptor = SnapshotDescriptor.construct(
snapshot_class=engine.InternalizedSnapshotClass,
snapshot_dimensions=engine.descriptor._dimensions)
self.engine = engine
super(_InternalizedEngineProxy, self).__init__(options={},
descriptor=descriptor)
def setup(self):
self.descriptor = SnapshotDescriptor.construct(
snapshot_class=ToySnapshot,
snapshot_dimensions={
'n_spatial': 1,
'n_atoms': 1
})
slow_options = {
'n_frames_max': 10000,
'engine_sleep': 100,
'name_prefix': "test",
'engine_directory': engine_dir
}
fast_options = {
'n_frames_max': 10000,
'engine_sleep': 0,
'name_prefix': "test",
'engine_directory': engine_dir
}
self.template = peng.toy.Snapshot(coordinates=np.array([[0.0]]),
velocities=np.array([[1.0]]))
self.slow_engine = ExampleExternalEngine(slow_options, self.descriptor,
self.template)
self.fast_engine = ExampleExternalEngine(fast_options, self.descriptor,
self.template)
self.ensemble = paths.LengthEnsemble(5)
def __init__(self, sequences, sleep_ms=0):
self.sequences = sequences
self.sleep_ms = sleep_ms
self.descriptor = SnapshotDescriptor.construct(
snapshot_class=ExternalMDSnapshot,
snapshot_dimensions={
'n_spatial': 2,
'n_atoms': 1
})
self.internalized_engine = _InternalizedEngineProxy(self)
def __init__(self, gro):
traj = md.load(gro)
self.topology = MDTrajTopology(traj.topology)
n_atoms = self.topology.n_atoms
n_spatial = self.topology.n_spatial
descriptor = SnapshotDescriptor.construct(
snapshot_class=ExternalMDSnapshot,
snapshot_dimensions={
'n_spatial': n_spatial,
'n_atoms': n_atoms
})
super(GroFileEngine, self).__init__(options={},
descriptor=descriptor,
template=None)