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Covalent Inhibitor Scan

Covalent inhibitor scan workflow - bond scan for a covalent inhibitor reaction.

CovalentInhibitorScanPoint dataclass 

CovalentInhibitorScanPoint(
    index: int,
    distance: float,
    molecule: Molecule,
    energy: float | None,
    uuid: str | None,
)

A point along the covalent inhibitor bond scan.

Parameters:

Name Type Description Default
index int

index of the point along the scan

 required
distance float

scanned bond distance, in Å

 required
molecule Molecule

Molecule at the point

 required
energy float | None

implicit-solvent single-point energy at this geometry, in Hartree

 required
uuid str | None

UUID of the scan-point calculation

 required

CovalentInhibitorScanResult dataclass 

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

Bases: WorkflowResult

Result from a covalent inhibitor scan workflow.

scan_points property 

scan_points: list[CovalentInhibitorScanPoint]

Points along the scan, ordered by scan index (scan_start to scan_stop).

get_energies 

get_energies() -> list[tuple[float, float | None]]

Get scan distances paired with single-point energies.

Returns:

Type Description
list[tuple[float, float | None]]

List of (distance, energy) tuples, in Å and Hartree respectively.

submit_covalent_inhibitor_scan_workflow 

submit_covalent_inhibitor_scan_workflow(
    protein: Protein | ProteinUUID,
    protein_reactive_atom_index: int,
    ligand_reactive_atom_index: int,
    ligand_smiles: str,
    settings: CovalentInhibitorScanSettings | None = None,
    name: str = "Covalent Inhibitor Scan 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 covalent inhibitor scan workflow to the API.

Parameters:

Name Type Description Default
protein Protein | ProteinUUID

covalently docked protein-ligand complex (protein plus the ligand as a non-polymer residue). Can be a UUID or a Protein object.

 required
protein_reactive_atom_index int

0-based index of the reacting protein atom, in PDB record order.

 required
ligand_reactive_atom_index int

0-based index of the reacting ligand atom, in PDB record order.

 required
ligand_smiles str

SMILES of the ligand, whose net charge sets the ligand charge of the QM cluster.

 required
settings CovalentInhibitorScanSettings | None

settings controlling the scan. Defaults to stjames.CovalentInhibitorScanSettings().

 None
name str

name of the workflow.

 'Covalent Inhibitor Scan 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
requests.HTTPError

if the request to the API fails.