Protein preparation

Protein preparation workflow - prepare protein structures for simulation.

ProteinPreparationResult `dataclass`

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

Bases: WorkflowResult

Result from a protein-preparation workflow.

prepared_protein_uuid `property`

prepared_protein_uuid: ProteinUUID | None

UUID of the prepared protein structure.

get_prepared_protein

get_prepared_protein() -> Protein

Fetch the prepared protein structure.

.. note:: Makes one API call on first access. Results are cached. Call clear_cache() to refresh.

Returns:

Type	Description
`Protein`	prepared Protein object

Raises:

Type	Description
`ValueError`	if the workflow has not produced a prepared protein

submit_protein_preparation_workflow

submit_protein_preparation_workflow(
    protein: Protein | ProteinUUID,
    add_missing_method: Literal["boltz_2", "pdbfixer"]
    | None = "boltz_2",
    cap_residues: Literal["ace_nme", "terminal_templates"]
    | None = "ace_nme",
    protonation_method: Literal[
        "openmm", "protonate_utils", "propka_3"
    ] = "openmm",
    pH: float = 7.4,
    retain_protonation: bool = True,
    retain_non_polymer: dict[str | int, str | None]
    | None = _DEFAULT_RETAIN_NON_POLYMER,
    name: str = "Protein Preparation 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

Submit a protein-preparation workflow to the API.

Full protein preparation can take around ten minutes, depending on the structure and settings. For a faster PDBFixer/OpenMM-only path, use Protein.prepare().

Parameters:

Name	Type	Description	Default
`protein`	`Protein \| ProteinUUID`	protein to prepare, as a UUID or Protein object	required
`add_missing_method`	`Literal['boltz_2', 'pdbfixer'] \| None`	method for adding missing atoms and residues before protonation; None skips this step	`'boltz_2'`
`cap_residues`	`Literal['ace_nme', 'terminal_templates'] \| None`	terminal-residue capping method; `"ace_nme"` requires an add-missing method and is incompatible with `"protonate_utils"`; None disables capping	`'ace_nme'`
`protonation_method`	`Literal['openmm', 'protonate_utils', 'propka_3']`	method for adding hydrogens	`'openmm'`
`pH`	`float`	pH used to determine protonation states	`7.4`
`retain_protonation`	`bool`	whether to retain existing protonation states	`True`
`retain_non_polymer`	`dict[str \| int, str \| None] \| None`	non-polymer residues to retain, keyed by residue name or 0-based residue index. Values are SMILES strings used for parameterization. Known ions and waters may map to None; other residues require a SMILES string. None removes all non-polymer residues.	`_DEFAULT_RETAIN_NON_POLYMER`
`name`	`str`	name of the workflow	`'Protein Preparation 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 settings are incompatible or a retained residue mapping is invalid
`requests.HTTPError`	if the request to the API fails

Protein preparation