find_results: Retrieve Specific Fields for Search Results from RCSB PDB

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

Retrieve Specific Fields for Search Results from RCSB PDB

Description

This function searches the Protein Data Bank (PDB) for entries related to a specified search term and retrieves specific information from those entries. It is useful for extracting targeted data from search results, such as citations, experimental methods, or structural details. The function leverages 'query_search' to perform the initial search and 'get_info' to fetch detailed data for each PDB entry.

Usage

find_results(search_term, field = "citation")

Arguments

search_term

A string specifying the term to search for in the PDB. This term can relate to various aspects of the PDB entries, such as keywords, molecular functions, protein names, or specific research areas.

field

A string indicating the specific field to retrieve for each search result. The default is "citation". The field should correspond to one of the following valid options: "citation" Information about the primary citation associated with the PDB entry. "audit_author" Details about the authors who contributed to the PDB entry. "cell" Cell dimensions and related crystallographic information. "diffrn" Information about the diffraction experiment. "diffrn_detector" Details about the detector used in the diffraction experiment. "diffrn_radiation" Radiation source details used in the diffraction experiment. "diffrn_source" Source of the radiation used in the experiment. "entry" Basic information about the PDB entry, including its identifier. "exptl" Details about the experimental methods used to determine the structure. "exptl_crystal" Information about the crystals used in the experiment. "exptl_crystal_grow" Details on the crystal growth conditions. "pdbx_sgproject" Information on the Structural Genomics Project. "pdbx_audit_revision_details" Details of any revisions made to the PDB entry. "pdbx_audit_revision_history" History of the revisions for the PDB entry. "pdbx_database_related" Related database entries. "pdbx_database_status" Current status of the PDB entry in the database. "rcsb_accession_info" Accession information for the PDB entry. "rcsb_entry_container_identifiers" Identifiers associated with the entry container. "rcsb_entry_info" General information about the PDB entry. "rcsb_primary_citation" Details of the primary citation for the PDB entry. "refine" Information about the refinement of the structure. "refine_hist" History of the refinement process. "refine_ls_restr" Details about the least-squares restraints used in refinement. "reflns" Information about the reflections used in the crystallographic experiment. "reflns_shell" Details about the shell reflections used in the experiment. "software" Software used in the structure determination process. "struct" Structural information about the PDB entry. "struct_keywords" Keywords associated with the structure. "symmetry" Symmetry information of the crystal structure. "rcsb_id" The RCSB ID of the PDB entry.

Details

This function is ideal for researchers who need to extract specific data fields from multiple PDB entries efficiently. The process involves two main steps:

1. **Search Query**: The function uses 'query_search' to find PDB entries that match the provided search term.

2. **Field Retrieval**: For each PDB ID returned by the search, 'get_info' is used to retrieve the specified field.

Error handling is robust, with informative messages provided when the search term yields no results, when an individual PDB entry cannot be retrieved, or when the specified field is not found in the retrieved data.

Value

A named list where each element's name is a PDB ID and its value is the information for the specified field from the corresponding search result. If no results are found, or if an error occurs during data retrieval, the function returns an empty list with appropriate warnings or error messages.

Examples

# Retrieve citation information for PDB entries related to CRISPR
crispr_citations <- find_results("CRISPR", field = "citation")
crispr_citations

rPDBapi documentation built on Oct. 19, 2024, 5:08 p.m.