GufeTokenizable — OpenFE documentation

class openfe.utils.GufeTokenizable(*args, **kwargs)#

Bases: ABC

Base class for all tokenizeable gufe objects.

Subclassing from this provides sorting, equality and hashing operators, provided that the class implements the _to_dict and _from_dict method.

This extra work in serializing is important for hashes that are stable across different Python sessions.

Methods

`copy_with_replacements`	Make a modified copy of this object.
`defaults`	Dict of default key-value pairs for this GufeTokenizable object.
`from_dict`	Generate an instance from full dict representation.
`from_keyed_dict`	Generate an instance from keyed dict representation.
`from_shallow_dict`	Generate an instance from shallow dict representation.
`to_dict`	Generate full dict representation, with all referenced GufeTokenizable objects also given in full dict representations.
`to_keyed_dict`	Generate keyed dict representation, with all referenced GufeTokenizable objects given in keyed representations.
`to_shallow_dict`	Generate shallow dict representation, with all referenced GufeTokenizable objects left intact.

Attributes

`key`
`logger`	Return logger adapter for this instance

copy_with_replacements(**replacements)#

Make a modified copy of this object.

Since GufeTokenizables are immutable, this is essentially a shortcut to mutate the object. Note that the keyword arguments it takes are based on keys of the dictionaries used in the the _to_dict/_from_dict cycle for this object; in most cases that is the same as parameters to __init__, but not always.

This will always return a new object in memory. So using obj.copy_with_replacements() (with no keyword arguments) is a way to create a shallow copy: the object is different in memory, but its attributes will be the same objects in memory as the original.

Parameters:: replacements (Dict) – keyword arguments with keys taken from the keys given by the output of this object’s to_dict method.

classmethod defaults()#

Dict of default key-value pairs for this GufeTokenizable object.

These defaults are stripped from the dict form of this object produced with to_dict(include_defaults=False) where default values are present.

classmethod from_dict(dct: Dict)#

Generate an instance from full dict representation.

Parameters:: dct (Dict) – A dictionary produced by to_dict to instantiate from. If an identical instance already exists in memory, it will be returned. Otherwise, a new instance will be returned.

classmethod from_keyed_dict(dct: Dict)#

Generate an instance from keyed dict representation.

Parameters:: dct (Dict) – A dictionary produced by to_keyed_dict to instantiate from. If an identical instance already exists in memory, it will be returned. Otherwise, a new instance will be returned.

classmethod from_shallow_dict(dct: Dict)#

Generate an instance from shallow dict representation.

Parameters:: dct (Dict) – A dictionary produced by to_shallow_dict to instantiate from. If an identical instance already exists in memory, it will be returned. Otherwise, a new instance will be returned.

property key#

property logger#: Return logger adapter for this instance

to_dict(include_defaults=True) → dict#

Generate full dict representation, with all referenced GufeTokenizable objects also given in full dict representations.

Parameters:: include_defaults (bool) – If False, strip keys from dict representation with values equal to those in defaults.

GufeTokenizable#

`GufeTokenizable`#