openpathsampling.snapshot_modifier.SnapshotModifier

class openpathsampling.snapshot_modifier.SnapshotModifier(subset_mask=None)

Abstract class for snapshot modification.

In general, a snapshot modifer will take a snapshot and return a modified version of that snapshot. These are useful for, e.g., two-way shooting or for committor analysis.

subset_mask

the subset to use (default None, meaning use all). The values select along the first axis of the input array. For example, in a typical shape=(n_atoms, 3) array, this will pick the atoms.

Type:

list of int or None

Note

It is tempting to use the various indexing tricks in numpy to get a view on the data, instead of using this subset_mask. However, this can be dangerous: note that fancy indexing copies the data, whereas normal indexing returns a proper view. See http://stackoverflow.com/a/4371049. Rather than play with fire here, we’ll just do something straightforward. We can try something more clever in the future.

__init__(subset_mask=None)

Methods

__init__([subset_mask])
apply_to_subset(full_array, modified[, ...])	Replaces elements of full_array according to the subset mask
args()	Return a list of args of the __init__ function of a class
base()	Return the most parent class actually derived from StorableObject
count_weaks()	Return number of objects subclassed from StorableObject still in memory
descendants()	Return a list of all subclassed objects
extract_subset(full_array[, subset])	Extracts elements from full_array according to self.subset_mask
fix_name()	Set the objects name to be immutable.
from_dict(dct)	Reconstruct an object from a dictionary representaiton
get_uuid()
idx(store)	Return the index which is used for the object in the given store.
named(name)	Name an unnamed object.
objects()	Returns a dictionary of all storable objects
probability_ratio(old_snapshot, new_snapshot)	Only here for backwards compatability, will raise in the future
reverse_uuid()
ruuid(uid)
set_observer(active)	(De-)Activate observing creation of storable objects
to_dict()	Convert object into a dictionary representation

Attributes

ACTIVE_LONG
CREATION_COUNT
INSTANCE_UUID
base_cls	Return the base class
base_cls_name	Return the name of the base class
cls	Return the class name as a string
default_name	Return the default name.
is_named	True if this object has a custom name.
name	Return the current name of the object.
observe_objects