R/GetpdbStructure.R

In Proteomicslab57357/UniprotR: Retrieving Information of Proteins from Uniprot

#' Connect and parse UniProt information.
#'
#' The function is work to retrieving GetpdbStructure and download it
#' to user directory.
#'
#' @param ProteinAccList input a vector of UniProt Accession/s
#'
#' @param directorypath path to save excel file containig results returened by the function.
#'
#' @usage GetpdbStructure(ProteinAccList , directorypath = NULL)
#'
#'
#' @export
#'
#' @author Mohmed Soudy \email{Mohamed.soudy@57357.com} and Ali Mostafa \email{ali.mo.anwar@std.agr.cu.edu.eg}
#'
GetpdbStructure <- function(ProteinAccList , directorypath = NULL)
{
  baseUrl <- "https://swissmodel.expasy.org/repository/uniprot/"
  message("Please wait we are processing your accessions ...")
  pb <- progress::progress_bar$new(total = length(ProteinAccList))
  
  for (ProteinAcc in ProteinAccList)
  {
    RequiredAcc <- paste0(baseUrl , ProteinAcc ,".pdb")
    Request_Response <- GET(RequiredAcc)
    if(Request_Response$status_code == 200)
    {
      download.file(RequiredAcc , paste0(directorypath , "//" , ProteinAcc,".pdb"))
    }
    else{
      HandleBadRequests(Request_Response$status_code)
    }
    pb$tick()
    
  }
}