LigandNetwork

class openfe.setup.LigandNetwork(edges: Iterable[LigandAtomMapping], nodes: Iterable[SmallMoleculeComponent] | None = None)

Bases: GufeTokenizable

A directed graph connecting many ligands according to their atom mapping

Parameters:

• edges (Iterable[LigandAtomMapping]) – edges for this network

• nodes (Iterable[SmallMoleculeComponent]) – nodes for this network

Methods

enlarge_graph	Create a new network with the given edges and nodes added
from_graphml	Create Network from GraphML string.
is_connected	Are all ligands in the network (indirectly) connected to each other
to_graphml	Return the GraphML string representing this Network.
to_rbfe_alchemical_network	param protocol:

Attributes

edges	A read-only view of the edges of the Network
graph	NetworkX graph for this network
nodes	A read-only view of the nodes of the Network

property edges: FrozenSet[LigandAtomMapping]

A read-only view of the edges of the Network

enlarge_graph(*, edges=None, nodes=None) → LigandNetwork

Create a new network with the given edges and nodes added

Parameters:

• edges (Iterable[LigandAtomMapping]) – edges to append to this network

• nodes (Iterable[SmallMoleculeComponent]) – nodes to append to this network

Returns:

a new network adding the given edges and nodes to this network

Return type:

Network

classmethod from_graphml(graphml_str: str)

Create Network from GraphML string. This is the primary deserialization mechanism for this class.

Parameters:

graphml_str (str) – GraphML string representation of a Network

Returns:

new network from the GraphML

Return type:

Network

property graph: MultiDiGraph

NetworkX graph for this network

is_connected() → bool

Are all ligands in the network (indirectly) connected to each other

A “False” value indicates that either some ligands have no edges or that there are separate networks that do not link to each other.

property nodes: FrozenSet[SmallMoleculeComponent]

A read-only view of the nodes of the Network

to_graphml() → str

Return the GraphML string representing this Network.

This is the primary serialization mechanism for this class.

Returns:

string representing this network in GraphML format

Return type:

str

to_rbfe_alchemical_network(solvent: SolventComponent, protein: ProteinComponent, protocol: Protocol, *, autoname: bool = True, autoname_prefix: str = 'easy_rbfe', **other_components)

Parameters:

• protocol (:class:Protocol) –

• autoname (bool) – whether to automatically name objects by the ligand name and state label

• autoname_prefix (str) – prefix for the autonaming; only used if autonaming is True

• other_components – additional non-alchemical components, keyword will be the string label for the component