get_compounds {PubChemR}

Retrieve Compounds from PubChem

Description

This function sends a request to the PubChem database to retrieve compound data based on specified parameters.

Usage

get_compounds(
  identifier,
  namespace = "cid",
  operation = NULL,
  searchtype = NULL,
  options = NULL
)

Arguments

identifier

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

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.

operation

The operation to be performed (default: NULL).

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'.

options

Additional parameters passed to get_json.

Value

An object of class 'PubChemInstanceList' and 'PC_Compounds' containing compound information from the PubChem database.

See Also

retrieve, instance

Examples

compound <- get_compounds(
  identifier = c("aspirin", "ibuprofen", "rstudio"),
  namespace = "name"
)

print(compound)

# Return results for selected compound.
instance(compound, "aspirin")
instance(compound, "rstudio")
# instance(compound, "unknown"). # returns error.

# Extract compound properties for the compound "aspirin".
# Use the 'retrieve()' function to extract specific slots from the compound list.
retrieve(instance(compound, "aspirin"), "props")