ProtocolDAG

class openfe.protocols.ProtocolDAG(*, protocol_units: list[ProtocolUnit], transformation_key: GufeKey | None, extends_key: GufeKey | None = None, name: str | None = None)

Bases: GufeTokenizable, DAGMixin

An executable directed acyclic graph (DAG) of ProtocolUnit objects.

A ProtocolDAG is composed of ProtocolUnit objects as well as how they depend on each other. A single ProtocolDAG execution should yield sufficient information to calculate a free energy difference (though perhaps not converged) between two ChemicalSystem objects.

A ProtocolDAG yields a ProtocolDAGResult when executed.

name

Optional identifier for this ProtocolDAGResult.

Type:

str

protocol_units

ProtocolUnit`s (given in DAG-dependency order) used to compute this `ProtocolDAGResult. Tasks are always listed after their dependencies.

Type:

list[ProtocolUnit]

graph

Graph of ProtocolUnit`s as nodes, with directed edges to each `ProtocolUnit’s dependencies.

Type:

nx.DiGraph

transformation_key

Key of the Transformation that this ProtocolDAG corresponds to, if applicable. This functions as a label for identifying the source of this ProtocolDAG. This label will be passed on to the ProtocolDAGResult resulting from execution of this ProtocolDAG.

Type:

Union[GufeKey, None]

extends_key

Key of the ProtocolDAGResult that this ProtocolDAG extends from. This functions as a label for identifying the source of this ProtocolDAG. This label will be passed on to the ProtocolDAGResult resulting from execution of this ProtocolDAG.

Type:

Optional[GufeKey]

Create a new ProtocolDAG.

Parameters:

• protocol_units (Iterable[ProtocolUnit]) – The ProtocolUnit`s that make up this `ProtocolDAG, with dependencies included as inputs.

• name (str) – Unique identifier for this ProtocolDAG.