get_info: Retrieve Information for a Given PDB ID

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

Retrieve Information for a Given PDB ID

Description

This function retrieves comprehensive information for a specified PDB (Protein Data Bank) entry by querying the RCSB PDB RESTful API. The function handles HTTP requests, processes JSON responses, and can manage legacy PDB identifiers. It is particularly useful for obtaining all available data related to a specific PDB entry, which can include metadata, structural details, experimental methods, and more.

Usage

get_info(pdb_id)

Arguments

pdb_id

A string specifying the PDB entry of interest. The 'pdb_id' should be a 4-character alphanumeric code, representing the unique identifier of a PDB entry (e.g., "1XYZ"). If a legacy PDB identifier is provided in the format 'PDB_ID:CHAIN_ID', it will be automatically converted to the new format for querying.

Details

The 'get_info' function is versatile and designed for researchers who need to extract detailed structural and experimental information from the RCSB PDB. The function is robust, providing error handling for various scenarios, including network failures, incorrect PDB IDs, and API errors. It automatically manages legacy PDB IDs, ensuring compatibility with the latest API standards.

The output is a structured list that can be easily parsed or manipulated for further analysis, making it an essential tool for bioinformaticians and structural biologists working with PDB data.

The function also offers flexibility in querying different parts of the RCSB PDB API by adjusting the 'url_root' parameter, allowing users to target specific datasets within the PDB.

Value

A list object (an ordered dictionary in R) containing detailed information about the specified PDB entry. The returned list includes various data fields, depending on the content available for the entry. For example, it may contain information about the structure's authors, resolution, experiment type, macromolecules, ligands, etc. If the data retrieval fails at any stage (e.g., network issues, invalid PDB ID, API downtime), the function will return 'NULL' and provide an informative error message.

Examples

pdb_info <- get_info(pdb_id = "1XYZ")
print(pdb_info)

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