mkt.databases.protvar.ProtvarScoreQuery

class mkt.databases.protvar.ProtvarScoreQuery(uniprot_id: str, pos: int, mut: str | None = None, url: str = 'https://www.ebi.ac.uk/ProtVar/api/score/<UNIPROT>/<POS>?mt=<MUT>', header: dict = <factory>)

Bases: RESTAPIClient

Class to interact with the ProtVar score API.

A single query returns scores for every available database (Conservation, EVE, ESM1b, AlphaMissense, popEVE). The response is parsed into ProtvarVariant objects exposed via variants:

• mut supplied -> a single variant keyed by that residue.

• mut is None -> one variant per possible substitution (keyed by residue).

Residue identity for the variant-level databases is recovered from popEVE, the only database whose payload carries the mutant residue (mt).

__init__(*args: Any, **kwargs: Any) → None

Methods

__eq__(other)	Return self==value.
__post_init__()
_build_variants()	Parse the flat score list into per-variant ProtvarVariant objects.
_stamp_from_response(res)	Record query datetime + cache provenance from a requests-cache response.
_stamp_now()	Record current UTC datetime; cache provenance unknown.
check_response(res)	Check the response status code for errors.
create_query_url()	Create URL for Protvar score API query.
get_scores()	Return all raw score dicts retained from the query.
get_variant([mt])	Return a single variant by mutant residue.
query_api()	Query the ProtVar score API and parse the response into variants.

Attributes

__dataclass_fields__
__dataclass_params__
__match_args__
__pydantic_config__
from_cache	Whether the most recent response was served from requests-cache.
mut	Mutant residue (1 or 3 letter code); optional.
query_datetime	UTC datetime the underlying network query was made (cache creation time if served from cache).
url	URL for Protvar score API query.
uniprot_id	Uniprot ID.
pos	Position in the protein where mutation resides.
header	Header for the API request.

_build_variants() → None

Parse the flat score list into per-variant ProtvarVariant objects.

create_query_url()

Create URL for Protvar score API query.

get_scores() → list[dict] | None

Return all raw score dicts retained from the query.

Returns:

All score dicts returned by the api, or None if the query failed.

Return type:

list[dict] | None

get_variant(mt: str | None = None) → ProtvarVariant | None

Return a single variant by mutant residue.

Parameters:

mt (str | None, optional) – Mutant residue to retrieve. If None and the query targeted a single variant, that sole variant is returned; otherwise None.

Returns:

The requested variant, or None if absent.

Return type:

ProtvarVariant | None

header: dict

Header for the API request.

mut: str | None = None

Mutant residue (1 or 3 letter code); optional. If None, scores for every possible substitution at this position are returned.

pos: int

Position in the protein where mutation resides.

query_api() → None

Query the ProtVar score API and parse the response into variants.

uniprot_id: str

Uniprot ID.

url: str = 'https://www.ebi.ac.uk/ProtVar/api/score/<UNIPROT>/<POS>?mt=<MUT>'

URL for Protvar score API query.