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Binding Affinity

Binding affinity workflow — SQM- and ML-based scoring of protein–ligand complexes.

BindingAffinityScore dataclass 

BindingAffinityScore(
    binding_affinity: float, strain: float | None
)

Binding affinity score for a single protein-ligand input.

Parameters:

Name Type Description Default
binding_affinity float

binding affinity in kcal/mol for SQM settings, or log10(M) for GNINA, AEV-PLIG, and NESSO settings.

 required
strain float | None

strain energy in kcal/mol, or None if not computed

 required

BindingAffinityResult dataclass 

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

Bases: WorkflowResult

Result from a binding affinity workflow.

scores property 

scores: list[BindingAffinityScore | None]

Binding affinity scores in input order, with None for failed inputs.

messages property 

messages: list[Message]

Any messages or warnings from the workflow.

submit_binding_affinity_workflow 

submit_binding_affinity_workflow(
    protein: Protein | ProteinUUID | None = None,
    ligand_residue_name: str | None = None,
    ligand_structures: list[StructureInput] | None = None,
    protein_sequences: list[ProteinSequence]
    | list[str]
    | None = None,
    ligand_smiles: list[str] | None = None,
    binding_affinity_settings: BindingAffinitySettings
    | None = None,
    name: str = "Binding Affinity Workflow",
    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 a binding affinity workflow to the API.

Scores protein-ligand inputs using SQM energies, GNINA, AEV-PLIG, or NESSO. Three input modes are supported:

Mode 1 — holo protein: protein already contains the bound ligand. Pass ligand_residue_name to identify which residue is the ligand vs. the receptor. Do not pass ligand_structures.

Mode 2 — apo protein + external poses: protein has no bound ligand. Pass ligand_structures with poses that are already in the protein's coordinate frame. Do not pass ligand_residue_name.

Mode 3 — NESSO sequence/SMILES input: NESSO-only (binding_affinity_settings must be NessoAffinitySettings); no PDB required. Pass protein_sequences instead of protein, and ligand_smiles instead of ligand_residue_name/ ligand_structures.

NESSO also accepts a protein PDB but uses only its protein sequence, not its 3D coordinates.

Parameters:

Name Type Description Default
protein Protein | ProteinUUID | None

protein structure. Can be input as a UUID or a Protein object. Required unless protein_sequences is set (mode 3).

 None
ligand_residue_name str | None

residue name identifying the ligand in a holo protein PDB (mode 1 only).

 None
ligand_structures list[StructureInput] | None

external ligand poses to score, already in the protein's coordinate frame. Must have 3D coordinates (mode 2 only).

 None
protein_sequences list[ProteinSequence] | list[str] | None

protein sequences to score against, in place of protein (mode 3, NESSO only).

 None
ligand_smiles list[str] | None

ligand SMILES to score, in place of ligand_residue_name/ ligand_structures (mode 3, NESSO only).

 None
binding_affinity_settings BindingAffinitySettings | None

settings controlling how binding affinity is computed: SinglePointEnergySettings (SQM), GninaAffinitySettings, AEVPLIGAffinitySettings, or NessoAffinitySettings. Defaults to SinglePointEnergySettings (PM6-D3H4X/COSMO optimization followed by PM6-D3H4X/COSMO2 single-point in water).

 None
name str

name of the workflow.

 'Binding Affinity Workflow'
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 folder arguments conflict.
pydantic.ValidationError

if the protein/ligand input combination is invalid.
requests.HTTPError

if the request to the API fails.