fetch_data: Fetch Data from RCSB PDB Using a JSON Query

In rPDBapi: A Comprehensive Interface for Accessing the Protein Data Bank

Fetch Data from RCSB PDB Using a JSON Query

Description

This function sends a GraphQL JSON query to the RCSB Protein Data Bank (PDB) to fetch data corresponding to a specified set of IDs. It is designed to handle the complexities of interacting with the PDB's GraphQL API, ensuring that errors in the query process are handled gracefully and that users are informed of any discrepancies in the expected and returned data.

Usage

fetch_data(json_query, data_type, ids)

Arguments

json_query	A JSON string representing the query to be sent to the PDB. This query must be well-formed and adhere to the GraphQL query structure required by the PDB's API. It typically includes details such as the fields to be retrieved and the conditions for data selection.
data_type	A string indicating the type of data to be fetched. While this parameter is not directly used in the function, it can provide context for the data being retrieved, such as "ENTRY", "ASSEMBLY", "POLYMER_ENTITY", etc.
ids	A character vector of identifiers for which data is being requested. These IDs should correspond to valid entries in the PDB and should match the data structure expected by the PDB's API.

Details

The function performs several checks and operations:

* It validates the 'json_query' to ensure that it is neither 'NULL' nor empty. * It attempts to send the query to the PDB's GraphQL endpoint using a helper function (assumed to be 'search_graphql'). * It checks the server's response to determine if the query was successful or if any errors were encountered. * If the data returned does not match the expected IDs, the function issues warnings and stops execution, providing details on the missing IDs. * The function ensures that the returned data is correctly named according to the provided IDs.

The function is particularly useful for developers and researchers who need to programmatically access and manipulate large datasets from the PDB. It abstracts away some of the complexity of directly interacting with the PDB's API, providing a more user-friendly interface for data retrieval.

Value

A list containing the data fetched from the PDB, with the names of the list elements set to the corresponding IDs. If any issues occur during the fetching process (e.g., if some IDs are not found), the function will return 'NULL' and provide informative error messages to help diagnose the problem.

rPDBapi documentation built on Sept. 11, 2024, 6:37 p.m.