KeyedChain — gufe documentation

class gufe.tokenization.KeyedChain(keyed_chain)#

Keyed chain representation encoder of a GufeTokenizable.

The keyed chain representation of a GufeTokenizable provides a topologically sorted list of gufe keys and GufeTokenizable keyed dicts that can be used to fully recreate a GufeTokenizable without the need for a populated TOKENIZATION_REGISTRY.

The class wraps around a list of tuples containing the gufe key and the keyed dict form of the GufeTokenizable.

Examples

We can create a keyed chain representation from any GufeTokenizable, such as:

>>> from gufe.tokenization import KeyedChain
>>> s = SolventComponent()
>>> keyed_chain = KeyedChain.gufe_to_keyed_chain_rep(s)
>>> keyed_chain
[('SolventComponent-26b4034ad9dbd9f908dfc298ea8d449f',
  {'smiles': 'O',
   'positive_ion': 'Na+',
   'negative_ion': 'Cl-',
   'ion_concentration': '0.15 molar',
   'neutralize': True,
   '__qualname__': 'SolventComponent',
   '__module__': 'gufe.components.solventcomponent',
   ':version:': 1})]

And we can do the reverse operation as well to go from a keyed chain representation back to a GufeTokenizable:

>>> KeyedChain(keyed_chain).to_gufe()
SolventComponent(name=O, Na+, Cl-)

Methods

`from_gufe`	Initialize a KeyedChain from a GufeTokenizable.
`from_keyed_chain_rep`	Initialize a KeyedChain from a keyed chain representation.
`gufe_keys`	Create a generator that iterates over the gufe keys in the KeyedChain.
`gufe_to_keyed_chain_rep`	Create the keyed chain representation of a GufeTokenizable.
`keyed_dicts`	Create a generator that iterates over the keyed dicts in the KeyedChain.
`to_gufe`	Initialize a GufeTokenizable.
`to_keyed_chain_rep`	Return the keyed chain representation of this object.

classmethod from_gufe(gufe_object: GufeTokenizable) → Self#: Initialize a KeyedChain from a GufeTokenizable.

classmethod from_keyed_chain_rep(keyed_chain: list[tuple[str, dict]]) → Self#: Initialize a KeyedChain from a keyed chain representation.

gufe_keys() → Generator[str, None, None]#: Create a generator that iterates over the gufe keys in the KeyedChain.

static gufe_to_keyed_chain_rep(gufe_object: GufeTokenizable) → list[tuple[str, dict]]#

Create the keyed chain representation of a GufeTokenizable.

This represents the GufeTokenizable as a list of two-element tuples containing, as their first and second elements, the gufe key and keyed dict form of the GufeTokenizable, respectively, and provides the underlying structure used in the KeyedChain class.

Parameters:: gufe_object – The GufeTokenizable for which the KeyedChain is generated.
Returns:: The keyed chain representation of a GufeTokenizable.
Return type:: key_and_keyed_dicts

keyed_dicts() → Generator[dict, None, None]#: Create a generator that iterates over the keyed dicts in the KeyedChain.

to_gufe() → GufeTokenizable#: Initialize a GufeTokenizable.

to_keyed_chain_rep() → list[tuple[str, dict]]#: Return the keyed chain representation of this object.

KeyedChain#

`KeyedChain`#