RBFE Graph

RBFE graph workflow - build perturbation graphs for relative binding free energy calculations.

RelativeBindingFreeEnergyGraphEdge dataclass

RelativeBindingFreeEnergyGraphEdge(
    ligand_a: str,
    ligand_b: str,
    core: list[tuple[int, int]] | None = None,
    score: float | None = None,
    ddg: float | None = None,
    ddg_err: float | None = None,
    complex_dg: float | None = None,
    complex_dg_err: float | None = None,
    solvent_dg: float | None = None,
    solvent_dg_err: float | None = None,
    vacuum_dg: float | None = None,
    vacuum_dg_err: float | None = None,
    failed: bool = False,
    complex_lambda_values: list[float] | None = None,
    complex_overlap_matrix: list[list[float]] | None = None,
)

An edge in an RBFE perturbation graph.

RelativeBindingFreeEnergyGraphResult dataclass

RelativeBindingFreeEnergyGraphResult(
    workflow_data: dict[str, Any],
    workflow_type: str,
    workflow_uuid: str,
    complete: bool = True,
)

Bases: WorkflowResult

Result from an RBFE graph construction workflow.

ligands property

ligands: dict[str, Molecule]

Ligand molecules keyed by identifier.

graph property

graph: RBFEGraph | None

The constructed RBFE graph, or None if not yet computed.

edges property

edges: list[RelativeBindingFreeEnergyGraphEdge]

Graph edges. Empty list if graph is not yet built.

submit_relative_binding_free_energy_graph_workflow

submit_relative_binding_free_energy_graph_workflow(
    ligands: dict[str, StructureInput],
    mode: Literal["greedy", "star_map"] = "greedy",
    hub_compound_id: str | None = None,
    greedy_scoring: Literal[
        "best", "jaccard", "dummy_atoms"
    ] = "best",
    greedy_k_min_cut: int = 3,
    refine_cutoff: float | None = None,
    seed_graph: RBFEGraph | None = None,
    generate_intermediate_ligands: bool = False,
    intermediate_max_dummy_atoms: int = 25,
    intermediate_min_dummy_atom_improvement: int = 5,
    name: str = "RBFE Graph",
    folder_uuid: str | None = None,
    folder: Folder | None = None,
    max_credits: int | None = None,
    webhook_url: str | None = None,
    is_draft: bool = False,
) -> Workflow

Submits an RBFE graph construction workflow to the API.

Builds a perturbation graph connecting ligands for relative binding free energy (RBFE) calculations.

Parameters:

Name	Type	Description	Default
ligands	dict[str, StructureInput]	Dictionary mapping ligand identifiers to molecules.	required
mode	Literal['greedy', 'star_map']	Graph construction strategy: "greedy" or "star_map".	'greedy'
hub_compound_id	str | None	Ligand identifier for the hub when mode="star_map".	None
greedy_scoring	Literal['best', 'jaccard', 'dummy_atoms']	Edge scoring heuristic for greedy mode: "best", "jaccard", or "dummy_atoms".	'best'
greedy_k_min_cut	int	Target edge-connectivity for greedy augmentation. Must be > 0.	3
refine_cutoff	float | None	Optional MCS similarity cutoff for graph refinement.	None
seed_graph	RBFEGraph | None	RBFE graph from a prior run to extend, as returned by a completed result's graph. Its existing edges (and any computed results) are preserved, and only edges for newly added ligands are built.	None
generate_intermediate_ligands	bool	Generate virtual intermediate ligands to make difficult edges easier.	False
intermediate_max_dummy_atoms	int	An edge with more dummy atoms than this is split when a generated intermediate brings both resulting legs back to at most this value.	25
intermediate_min_dummy_atom_improvement	int	Minimum reduction in the worst leg's dummy-atom count required for a generated intermediate to be accepted.	5
name	str	Name of the workflow.	'RBFE Graph'
folder_uuid	str | None	UUID of the folder to place the workflow in.	None
folder	Folder | None	Folder object to store the workflow in.	None
max_credits	int | None	Maximum number of credits to use for the workflow.	None
webhook_url	str | None	URL that Rowan will POST to when the workflow completes.	None
is_draft	bool	If True, submit the workflow as a draft without starting execution.	False

Returns:

Type	Description
Workflow	Workflow object representing the submitted workflow.

Raises:

Type	Description
ValueError	If both folder and folder_uuid are provided, if any ligand has no defined charge, or if the ligands do not all share the same formal charge.
requests.HTTPError	if the request to the API fails.