mkt.databases

Module in missense-kinase-toolkit for querying databases.

Modules

aligners	Pairwise and multiple-sequence aligner wrappers for mapping kinase sequences onto UniProt.
alphafold	Client for retrieving AlphaFold structure predictions.
api_schema	Base API client hierarchy (Swagger, REST, GraphQL) with query and cache provenance stamping.
app	Subpackage backing the missense-kinase-toolkit Streamlit app.
cancer_hotspots	Client and parser for the Cancer Hotspots database.
cbioportal	cBioPortal API client and extraction of missense kinase mutations, treatments, and panels.
chembl	ChEMBL molecule-search client for resolving drug names to ChEMBL IDs and metadata.
cli	Command-line entry points for mkt.databases.
colors	Color palettes and colormap helpers for amino acids and percentile-based plotting.
config	Environment-variable configuration for cBioPortal, OncoKB, and the requests cache.
conservation	Study-independent KLIFS hierarchical conservation of the human kinome.
datasets	Subpackage for kinase profiling dataset processing (Davis, PKIS2, DiscoverX).
hgnc	Client for the HGNC (HUGO Gene Nomenclature Committee) REST API.
io_utils	File I/O helpers for CSV/dataframe round-tripping, tar creation, and kinase-dict loading.
kinase_schema	Builders that assemble KinaseInfo objects from API and scraper data.
kincore	Parsing and harmonization of KinCore FASTA and CIF structure files, aligned to UniProt.
klifs	KLIFS API client for kinase names, pocket residues, and KLIFS region annotations.
log_config	Logging configuration helpers and argparse logging flags.
ncbi	Client for NCBI Entrez protein records.
oncokb	OncoKB API client for therapeutic levels, protein-change annotations, and the cancer gene list.
oncotree	OncoTree cancer-type ontology model and parsing.
open_targets	Open Targets GraphQL client for drug mechanism-of-action data.
pfam	Pfam API client and helper for locating kinase-domain boundaries.
plot	Plotting functions for kinase data.
plot_config	Configuration dataclasses for plot_dataset_data.py.
properties	Amino-acid property lookups and classification of amino-acid changes.
protvar	ProtVar API client for variant pathogenicity scores.
pssm	Position-specific residue statistics: background-relative information content with a substitution-aware (Henikoff) pseudocount prior.
pymol	Generation of PyMOL visualization scripts for kinase structures.
requests_wrapper	Cached HTTP session wrapper (requests-cache) with retry handling.
sasa	Solvent-accessible surface area (SASA) computation configs and residue-level calculation.
scrapers	Web scrapers for kinase data sources.
three_d_hotspots	Loader and parser for the 3D Hotspots database.
uniprot	UniProt clients for FASTA sequences and JSON records.
utils	General-purpose string, dataframe, and structure utility functions.
utils_requests	Small helpers for inspecting HTTP responses.