omnilab/pdb Référence de l’API

Omnilab\Pdb

PdbSource class

final class PdbSource extends HttpSource PdbSource.php:41

The Protein Data Bank, through the APIs of RCSB PDB: an entry by its PDB id (4HHB, or its extended form pdb_00004hhb) - its title, keywords, experimental method, resolution, weight, dates, primary citation and authors; its polymer entities (the chains: their description, strands, length, organism) and its ligands (their chemical component, formula, weight) as properties; the UniProt proteins of its chains, their organisms and its ligands as related things - a structure is not its protein, nor its ligand: the Collector follows none of them -; an image of its first assembly; and RCSB's full-text search.

Which API: the Data API's GraphQL endpoint (data.rcsb.org/graphql), one call for an entry with its entities, where the REST API takes one for the entry, one per polymer entity and one per ligand; RCSB's Search API (search.rcsb.org) for the search, which answers ids only, then one GraphQL call for the page's entries; the Data API's holdings for an entry removed from the archive (its replacement, when it has one).

No key. RCSB rate-limits every API, answers 429 beyond, and asks a client to start at a handful of calls a second: 0.25 s between two.

const BASE_URI = 'https://data.rcsb.org/'

const SEARCH_URI = 'https://search.rcsb.org/rcsbsearch/v2/query'

const THROTTLE = 0.25

Seconds between two calls: RCSB's "a handful a second".

const MAX_PER_PAGE = 100

The most entries one search page is asked for: their GraphQL answer grows with each.

PdbSource::__construct()

public function __construct(HttpClientInterface $http, readonly string $searchUri = self::SEARCH_URI, string $baseUri = self::BASE_URI, array $headers = [], float $throttle = self::THROTTLE)

PdbSource::getName()

public function getName(): string

PdbSource::capabilities()

public function capabilities(): array

PdbSource::entity()

public function entity(Identifier|string $id): ?Entity

An entry by its PDB id (4HHB, 4hhb, pdb:4HHB, pdb_00004hhb, its RCSB page): one call. An entry removed from the archive gives the one that replaced it, when only one did (two calls more); several, or none: null. A UniProt accession, a name or any other scheme is refused before any call: search() looks entries up by text.

PdbSource::search()

public function search(Query $query): Page

RCSB's full-text search over the experimental structures ("hemoglobin", "spike glycoprotein SARS-CoV-2"), the best first, page by offset: the Search API's ids, then their entries in one GraphQL call. A domain other than biology answers nothing.

PdbSourceFactory class

final class PdbSourceFactory extends SourceFactory PdbSourceFactory.php:22

The Protein Data Bank, through RCSB PDB's APIs: an entry by its PDB id - its title, method, resolution, dates, citation, its polymer entities with their UniProt proteins and organisms, its ligands with their chemical identifiers - and RCSB's full-text search - no key needed.

options: mailto: 'support@glitchr.io' # in the User-Agent: whom RCSB writes to before it blocks a caller throttle: 0.25 # seconds between two calls: RCSB asks to start at a handful a second, and answers 429 beyond its limit base_uri: 'https://data.rcsb.org/' # the Data API: GraphQL, and the holdings of removed entries search_uri: 'https://search.rcsb.org/rcsbsearch/v2/query' # the Search API

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