rPDBapi (version 2.1.1)

query_search: Search Query Function

Description

This function performs a search query against the RCSB Protein Data Bank using their REST API. It allows for various types of searches based on the provided parameters.

Usage

query_search(
  search_term,
  query_type = "full_text",
  return_type = "entry",
  scan_params = NULL,
  num_attempts = 1,
  sleep_time = 0.5
)

Value

Depending on the return_type, it either returns a list of PDB IDs (if "entry") or the full response from the API.

Arguments

search_term

A string specifying the term to search in the database.

query_type

A string specifying the type of query to perform. Supported values include "full_text", "PubmedIdQuery", "TreeEntityQuery", "ExpTypeQuery", "AdvancedAuthorQuery", "OrganismQuery", "pfam", and "uniprot". Default is "full_text".

return_type

A string specifying the type of search result to return. Possible values are "entry" (default) and "polymer_entity".

scan_params

Additional parameters for the scan, provided as a list. This is `NULL` by default and typically only used for advanced queries.

num_attempts

An integer specifying the number of attempts to try the query in case of failure.

sleep_time

A numeric value specifying the time in seconds to wait between attempts.

Examples

# Get a list of PDBs for a specific search term
# \donttest{
# Search Functions by Specific Terms
pdbs <- query_search("ribosome")
head(pdbs)

# Search by PubMed ID Number
pdbs_by_pubmedid <- query_search(search_term = 27499440, query_type = "PubmedIdQuery")
head(pdbs_by_pubmedid)

# Search by source organism using NCBI TaxId
pdbs_by_ncbi_taxid <- query_search(search_term = "6239", query_type = "TreeEntityQuery")
head(pdbs_by_ncbi_taxid)

# Search by Experimental Method
pdbs = query_search(search_term = 'SOLID-STATE NMR', query_type='ExpTypeQuery')
head(pdbs)

pdbs = query_search(search_term = '4HHB', query_type="structure")
head(pdbs)

## Advanced Searches

# Search by Author
pdbs = query_search(search_term = 'Rzechorzek, N.J.', query_type='AdvancedAuthorQuery')
head(pdbs)

# Search by Organism
pdbs = query_search(search_term = "Escherichia coli", query_type="OrganismQuery")
head(pdbs)

# Search by Uniprot ID (Escherichia coli beta-lactamase)
pdbs = query_search(search_term = "P0A877", query_type="uniprot")
head(pdbs)

# Search by PFAM number (protein kinase domain)
pdbs = query_search(search_term = "PF00069", query_type="pfam")
head(pdbs)
# }