Retrieve PubChem compound information

This function retrieves compound information from PubChem using the PubChem REST API. Used by other functions to retrieve compound information.

Usage

getPubchemCompound(
  ids,
  from = "cid",
  to = "property",
  properties = c("Title", "InChIKey"),
  raw = FALSE,
  query_only = FALSE,
  output = "JSON",
  ...
)

Arguments

ids

A vector of compound identifiers.

from

The source namespace of the compound identifiers. Default is 'cid'.

to

The target namespace for the compound information. Default is 'property'.

properties

A character vector specifying the properties to retrieve.

raw

Logical indicating whether to return the raw query results. Default is FALSE.

query_only

Logical indicating whether to only perform the query without retrieving the results. Default is FALSE.

output

The format of the query results. Default is 'JSON'.

...

Additional arguments to be passed to the query_pubchem_rest function.

Value

A data.table containing the retrieved compound information.

Examples

properties <- c("Title", "MolecularFormula", "InChIKey", "CanonicalSMILES")
getPubchemCompound(c(3672, 176870), from = "cid", to = "property", properties = properties)
#>       CID MolecularFormula                                   ConnectivitySMILES
#>     <int>           <char>                                               <char>
#> 1:   3672         C13H18O2                        CC(C)CC1=CC=C(C=C1)C(C)C(=O)O
#> 2: 176870       C22H23N3O4 COCCOC1=C(C=C2C(=C1)C(=NC=N2)NC3=CC=CC(=C3)C#C)OCCOC
#>                       InChIKey            Title
#>                         <char>           <char>
#> 1: HEFNNWSXXWATRW-UHFFFAOYSA-N Ibuprofen, (+-)-
#> 2: AAKJLRGGTJKAMG-UHFFFAOYSA-N        Erlotinib