download {PubChemR}

Download Content from PubChem and Save to a File

Description

This function sends a request to PubChem to retrieve content in the specified format for a given identifier. It then writes the content to a specified file path.

Usage

download(
  filename = NULL,
  outformat,
  path,
  identifier,
  namespace = "cid",
  domain = "compound",
  operation = NULL,
  searchtype = NULL,
  overwrite = FALSE,
  options = NULL
)

Arguments

filename

a character string specifying the file name to be saved. If not specified, a default file name "file" is used.

outformat

A character string specifying the desired output format (e.g., "sdf", "json").

path

A character string specifying the path where the content should be saved.

identifier

A vector of positive integers (e.g. cid, sid, aid) or identifier strings (source, inchikey, formula). In some cases, only a single identifier string (name, smiles, xref; inchi, sdf by POST only).

namespace

Specifies the namespace for the query. For the 'compound' domain, possible values include 'cid', 'name', 'smiles', 'inchi', 'sdf', 'inchikey', 'formula', 'substructure', 'superstructure', 'similarity', 'identity', 'xref', 'listkey', 'fastidentity', 'fastsimilarity_2d', 'fastsimilarity_3d', 'fastsubstructure', 'fastsuperstructure', and 'fastformula'. For other domains, the possible namespaces are domain-specific.

domain

Specifies the domain of the query. Possible values are 'substance', 'compound', 'assay', 'gene', 'protein', 'pathway', 'taxonomy', 'cell', 'sources', 'sourcetable', 'conformers', 'annotations', 'classification', and 'standardize'.

operation

Specifies the operation to be performed on the input records. For the 'compound' domain, possible operations include 'record', 'property', 'synonyms', 'sids', 'cids', 'aids', 'assaysummary', 'classification', 'xrefs', and 'description'. The available operations are domain-specific.

searchtype

Specifies the type of search to be performed. For structure searches, possible values are combinations of 'substructure', 'superstructure', 'similarity', 'identity' with 'smiles', 'inchi', 'sdf', 'cid'. For fast searches, possible values are combinations of 'fastidentity', 'fastsimilarity_2d', 'fastsimilarity_3d', 'fastsubstructure', 'fastsuperstructure' with 'smiles', 'smarts', 'inchi', 'sdf', 'cid', or 'fastformula'.

overwrite

A logical value indicating whether to overwrite the file if it already exists. Default is FALSE.

options

Additional arguments.

Value

No return value. The function writes the content to the specified file path and prints a message indicating the save location.

Examples

# Download JSON file for the compound "aspirin" into "Aspirin.JSON"
# A folder named "Compound" will be created under current directory"
download(
  filename = "Aspirin",
  outformat = "json",
  path = "./Compound",
  identifier = "aspirin",
  namespace = "name",
  domain = "compound",
  overwrite = TRUE
)

# Remove downloaded files and folders.
file.remove("./Compound/Aspirin.json")
file.remove("./Compound/")