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deeporigin.drug_discovery.uniprot_discovery

Bases: Execution, SyncExecutableMixin

Rank experimental PDBs for a UniProt accession via the platform tool.

Call :meth:run for ranked candidates. Call :meth:import_proteins to sync recommended or selected PDB IDs into a project with uniprot_accession persisted.

Attributes

candidates property 

candidates: list[UniprotDiscoveryCandidate] | None

Cached candidates from the last successful :meth:run, if any.

name instance-attribute 

name = name

project_id property 

project_id: str | None

Optional project id used as a default for :meth:import_proteins.

tool_key class-attribute instance-attribute 

tool_key: str = TOOL_KEYS_AND_VERSIONS["uniprot_discovery"][
    "tool_key"
]

tool_version instance-attribute 

tool_version = tool_version

uniprot_accession property 

uniprot_accession: str

UniProtKB accession configured for this job.

Methods:

from_dto classmethod 

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

Construct a UniprotDiscovery from a tools execution DTO.

Restores uniprot_accession 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.

 None

Returns:

Type Description
Self

A UniprotDiscovery with id and domain inputs restored.

Raises:

Type Description
ValueError

If stored inputs lack uniprot_accession.

import_proteins 

import_proteins(
    pdb_ids: list[str] | None = None,
    *,
    project_id: str | None = None
) -> list[Protein]

Download and sync selected (or recommended) PDB candidates.

Runs :meth:run if candidates are not already cached. Requires a resolvable project id. Each protein is synced with :attr:~deeporigin.drug_discovery.structures.protein.Protein.uniprot_accession set from this job.

Parameters:

Name Type Description Default
pdb_ids list[str] | None

PDB IDs to import. Must appear in this accession's candidates. When None, imports the single recommended candidate.

 None
project_id str | None

Project to sync into. Falls back to the instance project_id, then client.project_id.

 None

Returns:

Name Type Description
Synced list[Protein]

class:~deeporigin.drug_discovery.structures.protein.Protein
list[Protein]

instances (one per selected PDB ID).

Raises:

Type Description
DeepOriginException

If project is missing, candidates are empty, selection is invalid, or sync fails.

run 

run(
    *,
    quote: bool = False,
    approve_amount: int | None = None
) -> list[UniprotDiscoveryCandidate] | None

Run UniProt discovery synchronously and return ranked candidates.

Parameters:

Name Type Description Default
quote bool

Shorthand for approve_amount=-1. Returns None when the platform returns a quotation.

 False
approve_amount int | None

Spend cap forwarded as approveAmount.

 None

Returns:

Name Type Description
Ranked list[UniprotDiscoveryCandidate] | None

class:UniprotDiscoveryCandidate rows (possibly empty), or
list[UniprotDiscoveryCandidate] | None

None for quote-only responses.

Raises:

Type Description
DeepOriginException

If the execution does not succeed or jobOutputs.candidates is missing/invalid.