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.
submit_relative_binding_free_energy_graph_workflow
submit_relative_binding_free_energy_graph_workflow(ligands: Mapping[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[RelativeBindingFreeEnergyGraphResult]
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
|
Mapping[str, StructureInput]
|
dictionary mapping ligand identifiers to molecules |
required |
mode
|
Literal['greedy', 'star_map']
|
graph construction strategy: |
'greedy'
|
hub_compound_id
|
str | None
|
ligand identifier for the hub when |
None
|
greedy_scoring
|
Literal['best', 'jaccard', 'dummy_atoms']
|
edge scoring heuristic for greedy mode:
|
'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 |
None
|
generate_intermediate_ligands
|
bool
|
generate virtual intermediate ligands to make difficult edges easier |
False
|
intermediate_max_dummy_atoms
|
int
|
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
|
destination folder |
None
|
max_credits
|
int | None
|
maximum credits for the workflow |
None
|
webhook_url
|
str | None
|
URL that Rowan will POST to when the workflow completes |
None
|
is_draft
|
bool
|
save as a draft without starting execution |
False
|
Returns:
| Type | Description |
|---|---|
Workflow[RelativeBindingFreeEnergyGraphResult]
|
submitted workflow |
Raises:
| Type | Description |
|---|---|
ValueError
|
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 |
HTTPStatusError
|
request to the API fails |