openpathsampling.snapshot_modifier.SnapshotModifier

class openpathsampling.snapshot_modifier.SnapshotModifier(subset_mask=None)[source]

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)[source]

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

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