Source code for openpathsampling.storage.stores.trajectory

from openpathsampling.engines.trajectory import Trajectory
from openpathsampling.netcdfplus import ObjectStore, LoaderProxy


[docs]class TrajectoryStore(ObjectStore):
[docs] def __init__(self): super(TrajectoryStore, self).__init__(Trajectory)
def to_dict(self): return {} def _save(self, trajectory, idx): self.vars['snapshots'][idx] = trajectory store = self.storage.snapshots for frame, snapshot in enumerate(trajectory.iter_proxies()): if type(snapshot) is not LoaderProxy: loader = store.proxy(snapshot) trajectory[frame] = loader def mention(self, trajectory): """ Save a trajectory and store its snapshots only shallow This will mention the ids of all snapshots in the file but not save the content of all the snapshots. This way you can store CV values if you want Parameters ---------- trajectory : :class:`openpathsampling.Trajectory` """ snap_store = self.storage.snapshots current_mention = snap_store.only_mention snap_store.only_mention = True self.save(trajectory) snap_store.only_mention = current_mention def _load(self, idx): trajectory = Trajectory(self.vars['snapshots'][idx]) return trajectory def cache_all(self): """Load all samples as fast as possible into the cache """ if not self._cached_all: idxs = range(len(self)) snaps = self.vars['snapshots'][:] [self.add_single_to_cache(i, j) for i, j in zip( idxs, snaps)] self._cached_all = True def add_single_to_cache(self, idx, snaps): """ Add a single object to cache by json Parameters ---------- idx : int the index where the object was stored snaps : list of `BaseSnapshot` json string the represents a serialized version of the stored object """ if idx not in self.cache: obj = Trajectory(snaps) self._get_id(idx, obj) self.cache[idx] = obj self.index[obj.__uuid__] = idx return obj def snapshot_indices(self, idx): """ Load snapshot indices for trajectory with ID 'idx' from the storage Parameters ---------- idx : int ID of the trajectory Returns ------- list of int trajectory indices """ # get the values return self.variables['snapshots'][idx].tolist() def iter_snapshot_indices(self): """ Return an iterator over the lists of snapshot indices for all trajectories in the storage Returns ------- Iterator the iterator """ for snap_idx in range(len(self)): yield self.snapshot_indices(snap_idx) def initialize(self, units=None): super(TrajectoryStore, self).initialize() # index associated storage in class variable for all Trajectory # instances to access self.create_variable( 'snapshots', 'lazyobj.snapshots', dimensions=('...',), description="trajectory[trajectory][frame] is the snapshot index " "(0..nspanshots-1) of frame 'frame' of trajectory " "'trajectory'.", chunksizes=(65536,) )