mkt.databases.kinase_schema.KinaseInfoGenerator

class mkt.databases.kinase_schema.KinaseInfoGenerator(*, hgnc_name: str, uniprot_id: ~typing.Annotated[str, ~pydantic.types.StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^[A-Z][0-9][A-Z0-9]{3}[0-9](_[12])?(_[12])?$)] | ~typing.Annotated[str, ~pydantic.types.StringConstraints(strip_whitespace=None, to_upper=None, to_lower=None, strict=None, min_length=None, max_length=None, pattern=^[A-Z][0-9][A-Z][A-Z0-9]{2}[0-9][A-Z][A-Z0-9]{2}[0-9](_[12])?(_[12])?$)], uniprot: ~mkt.schema.kinase_schema.UniProt, kinhub: ~mkt.schema.kinase_schema.KinHub | None = None, klifs: ~mkt.schema.kinase_schema.KLIFS | None = None, pfam: ~mkt.schema.kinase_schema.Pfam | None = None, kincore: ~mkt.schema.kinase_schema.KinCore | None = None, KLIFS2UniProtIdx: dict[str, int | None] | None = None, KLIFS2UniProtSeq: dict[str, str | None] | None = None, bool_offset: bool = True)

Bases: KinaseInfo

Pydantic model for kinase information.

__init__(**data: Any) → None

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Methods

_klifs_uniprot_idx_bounds()	Return the min and max non-None UniProt indices in KLIFS2UniProtIdx.
_reconcile_kd_bound_with_klifs(bound, ...)	Reconcile an adjudicated kinase domain bound with the KLIFS pocket.
adjudicate_group([bool_verbose])	Adjudicate group based on available data.
adjudicate_kd_end([int_max_gap, bool_verbose])	Adjudicate kinase domain end based on available data.
adjudicate_kd_sequence([bool_verbose])	Adjudicate kinase domain sequence based on available data.
adjudicate_kd_start([int_max_gap, bool_verbose])	Adjudicate kinase domain start based on available data.
check_molecular_brake_against_canonical()	Check this kinase's molecular brake residues against the canonical identities.
extract_sequence_from_cif([bool_verbose])	Extract sequence from CIF if available.
generate_kincore2uniprot_alignment()	Generate dictionary mapping KinCore to UniProt indices.
generate_klifs2uniprot_dict()	Generate dictionary mapping KLIFS to UniProt indices.
is_lipid_kinase()	Return boolean if a lipid kinase.
is_pseudogene()	Return boolean if a pseudogene.
is_pseudokinase()	Return boolean if a (predicted) pseudokinase.
return_molecular_brake_residues()	Return this kinase's residues at the molecular brake KLIFS positions.
standardize_offset(idx_in)	Standardize offset where necessary.
validate_klifs2uniprotidx(value)	Validate KLIFS2UniProtIdx dictionary to include all regions since TOML doesn't save None.
validate_klifs2uniprotseq(value)	Validate KLIFS2UniProtSeq dictionary to include all regions since TOML doesn't save None.

Attributes

bool_offset	Whether to use 1-based indexing (True) or 0-based indexing (False).
hgnc_name
uniprot_id
uniprot
kinhub
klifs
pfam
kincore
KLIFS2UniProtIdx
KLIFS2UniProtSeq

KLIFS2UniProtIdx: dict[str, int | None] | None

KLIFS2UniProtSeq: dict[str, str | None] | None

bool_offset: bool

Whether to use 1-based indexing (True) or 0-based indexing (False). Default is True.

Type:

bool

generate_kincore2uniprot_alignment() → Self

Generate dictionary mapping KinCore to UniProt indices.

generate_klifs2uniprot_dict() → Self

Generate dictionary mapping KLIFS to UniProt indices.

hgnc_name: str

kincore: KinCore | None

kinhub: KinHub | None

klifs: KLIFS | None

pfam: Pfam | None

standardize_offset(idx_in: int) → int

Standardize offset where necessary.

Parameters:

idx_in (int) – Index to standardize.

Returns:

Standardized index.

Return type:

int

uniprot: UniProt

uniprot_id: SwissProtIDSuffix | TrEMBLIDSuffix