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deeporigin.drug_discovery.protein_prep

ProteinPrep drives platform tool deeporigin.protein-prep to clean a protein structure. The workflow is async-only: start(), then wait() / watch(), then get_results() (an in-memory Protein). There is no run() and no quote.

ProteinPrep -- async-only execution for expert protein preparation.

Usage::

prep = ProteinPrep(protein, pdb_id="1EBY")  # pdb_id inferred if protein.pdb_id is set
prep.start()
prep.wait()
prepared = prep.get_results()  # in-memory Protein; id is None

Classes

ProteinPrep

Bases: Execution, AsyncExecutableMixin, NotebookWatchMixin

Prepare a protein structure via deeporigin.protein-prep (async-only).

Submit with :meth:start, track with :meth:wait / :meth:watch / :meth:sync, then load an in-memory :class:Protein from :meth:get_results. There is no run(). Quoting is unused (billing is skipped); do not pass quote=True.

Attributes:

Name Type Description
protein Protein

Input protein structure (unchanged after the run).
pdb_id str

4-character PDB ID used for loop-modelling templates.
keep_chain_ids list[str]

Chain IDs to keep; empty means all chains.
keep_cofactor_ids list[str]

Cofactor/metal residue names to keep; empty keeps none.
keep_water_residue_names list[str]

Water residue-name classes to keep; empty keeps none.
remove_ligand_ids list[str]

Ligand residue names to remove during cleanup.

Attributes

keep_chain_ids property 
keep_chain_ids: list[str]

Protein chain IDs to keep; empty means all chains.

keep_cofactor_ids property 
keep_cofactor_ids: list[str]

Cofactor/metal residue names to keep; empty keeps none.

keep_water_residue_names property 
keep_water_residue_names: list[str]

Water residue-name classes to keep; empty keeps none.

pdb_id property 
pdb_id: str

4-character PDB ID used for loop-modelling templates.

protein property 
protein: Protein

Input protein structure used for preparation.

remove_ligand_ids property 
remove_ligand_ids: list[str]

Ligand residue names to remove during cleanup.

tool_key class-attribute instance-attribute 
tool_key: str = TOOL_KEYS_AND_VERSIONS["protein_prep"][
    "tool_key"
]
tool_version instance-attribute 
tool_version = tool_version

Methods:

from_dto classmethod 
from_dto(
    dto: dict[str, Any],
    *,
    client: DeepOriginClient | None = None
) -> Self

Construct a ProteinPrep from a tools execution DTO.

Rehydrates protein, pdb_id, and keep/remove lists from userInputs (falling back to inputs).

Parameters:

Name Type Description Default
dto dict[str, Any]

Execution payload (same shape as client.executions.get).

 required
client DeepOriginClient | None

Optional API client. Uses the default if not provided.

 None

Returns:

Type Description
Self

A ProteinPrep with id, lifecycle fields, and domain inputs set.

Raises:

Type Description
ValueError

If pdb_id is missing from stored inputs.
get_results 
get_results(dto: dict[str, Any] | None = None) -> Protein

Load the prepared protein as an in-memory :class:Protein.

Tries result-explorer rows for this execution (result_type=preparedprotein), then jobOutputs.protein. Does not PATCH or create a proteins-table record; the returned Protein has id is None and remote_path set to the prepared PDB.

Parameters:

Name Type Description Default
dto dict[str, Any] | None

Optional execution payload. Passing it avoids an extra GET when the result-explorer path fails but jobOutputs is already in hand.

 None

Returns:

Type Description
Protein

An in-memory :class:Protein for the prepared structure.

Raises:

Type Description
ValueError

If :attr:id is unset.
DeepOriginException

If no prepared PDB path could be loaded.