openpathsampling.collectivevariables.GeneratorCV

class openpathsampling.collectivevariables.GeneratorCV(name, generator, cv_time_reversible=False, cv_requires_lists=False, cv_wrap_numpy_array=False, cv_scalarize_numpy_singletons=False, **kwargs)[source]

Turn a callable class or function generating a callable object into a CV

The class instance will be called with snapshots. The instance itself will be created using the given **kwargs.

__init__(name, generator, cv_time_reversible=False, cv_requires_lists=False, cv_wrap_numpy_array=False, cv_scalarize_numpy_singletons=False, **kwargs)[source]
Parameters:
  • name

  • generator (callable class) – a class where instances have a __call__ attribute

  • cv_time_reversible

  • cv_requires_lists

  • cv_wrap_numpy_array

  • cv_scalarize_numpy_singletons

  • **kwargs – additional arguments which should be given to c (for example, the atoms which define a specific distance/angle). Finally an instance instance = cls(**kwargs) is created when the CV is created and using the CV will call instance(snapshots)

Notes

Right now you cannot store user-defined classes. Only classes from external packages can be used.

Methods

__init__(name, generator[, ...])

args()

Return a list of args of the __init__ function of a class

base()

Return the most parent class actually derived from StorableObject

cache_all()

Sync this CV with attached storages

count_weaks()

Return number of objects subclassed from StorableObject still in memory

descendants()

Return a list of all subclassed objects

disable_diskcache()

enable_diskcache()

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_cache_store(value_store)

Attach store variables to the collective variables.

set_observer(active)

(De-)Activate observing creation of storable objects

str_chain()

Return a string representation of the chain of dicts called.

sync()

Sync this CV with the attached storages

to_dict()

Convert object into a dictionary representation

with_diskcache([template, chunksize, ...])

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.

generator

instance

is_named

True if this object has a custom name.

name

Return the current name of the object.

observe_objects

passing_chain

Return a list of chaindicts in order they will be tried.