R/read_full_chemdes.R

In jack-davison/chemdesr: Obtain Data from the ChemDes Platform

#' Read Full ChemDes
#'
#' @description This function scrapes all available chemical information from
#' ChemDes, a free web-based platform for the calculation of molecular
#' descriptors and fingerprints. This is effectively just a wrapper around
#' \code{read_chemdes} which automatically reads in Chemopy, CDK, RDKit, Pybel,
#' and PaDEL data for the given smiles.
#'
#' @param smile A simplified molecular-input line-entry system ("SMILES") string.
#' @param chatty TRUE/FALSE. If TRUE, will print messages to the console
#' updating you of the stage of scraping.
#'
#' @author Jack Davison, \email{jd1184@york.ac.uk}
#' @return A "wide" tibble of chemical information, labelled with the SMILES string.
#' @export

read_full_chemdes <- function(smile, chatty = F) {
  chemopy <- chemdesr::read_chemdes(smile = smile, desc = "chemopy")
  if (chatty) {
    message(paste(smile, "Chemopy Done."))
  }

  cdk <- chemdesr::read_chemdes(smile = smile, desc = "cdk")
  if (chatty) {
    message(paste(smile, "CDK Done."))
  }

  rdk <- chemdesr::read_chemdes(smile = smile, desc = "rdk")
  if (chatty) {
    message(paste(smile, "RDKit Done."))
  }

  pybel <- chemdesr::read_chemdes(smile = smile, desc = "pybel")
  if (chatty) {
    message(paste(smile, "Pybel Done."))
  }

  padel <- chemdesr::read_chemdes(smile = smile, desc = "padel")
  if (chatty) {
    message(paste(smile, "PaDEL Done."))
  }

  all <- chemopy %>%
    dplyr::inner_join(cdk, by = "smile") %>%
    dplyr::inner_join(rdk, by = "smile") %>%
    dplyr::inner_join(pybel, by = "smile") %>%
    dplyr::inner_join(padel, by = "smile") %>%
    dplyr::relocate(smile) %>%
    dplyr::tibble()

  if (chatty) {
    message(paste(smile, "Data Combined."))
  }

  return(all)
}