R/203-getProtRCSBPDB.R

In Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

#' Retrieve Protein Sequence in PDB Format from RCSB PDB
#'
#' Retrieve Protein Sequence in PDB Format from RCSB PDB
#'
#' This function retrieves protein sequences in PDB format from RCSB PDB.
#'
#' @param id A character vector, as the protein ID.
#' @param parallel An integer, the parallel parameter, indicates how many
#'                 process the user would like to use for retrieving
#'                 the data (using RCurl), default is \code{5}.
#'                 For regular cases, we recommend a number less than \code{20}.
#'
#' @return A list, each component contains one of the protein sequences
#' in PDB format.
#'
#' @keywords getProt getPDBFromRCSBPDB PDB
#'
#' @aliases getPDBFromRCSBPDB
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @seealso See \code{\link{getSeqFromRCSBPDB}} for retrieving protein
#' represented by amino acid sequence from the RCSB PDB database.
#'
#' @export getPDBFromRCSBPDB
#'
#' @importFrom RCurl getURLAsynchronous
#'
#' @examples
#' id = c('4HHB', '4FF9')
#' \donttest{
#' getPDBFromRCSBPDB(id)}

getPDBFromRCSBPDB = function (id, parallel = 5) {

  # example id : 4HHB
  # example url: https://files.rcsb.org/view/4HHB.pdb

  pdbURL = paste0('https://files.rcsb.org/view/', id, '.pdb')

  pdbTxt = getURLAsynchronous(url = pdbURL, perform = parallel)

  return(pdbTxt)

}

#' Retrieve Protein Sequence from RCSB PDB
#'
#' Retrieve Protein Sequence from RCSB PDB
#'
#' This function retrieves protein sequences from RCSB PDB.
#'
#' @param id A character vector, as the protein ID.
#' @param parallel An integer, the parallel parameter, indicates how many
#'                 process the user would like to use for retrieving
#'                 the data (using RCurl), default is \code{5}.
#'                 For regular cases, we recommend a number less than \code{20}.
#'
#' @return A list, each component contains one of the protein represented by
#' amino acid sequence(s).
#'
#' @keywords getProt getSeqFromRCSBPDB PDB
#'
#' @aliases getSeqFromRCSBPDB
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @seealso See \code{\link{getPDBFromRCSBPDB}} for retrieving protein
#' in PDB format from the RCSB PDB database.
#'
#' @export getSeqFromRCSBPDB
#'
#' @importFrom RCurl getURLAsynchronous
#'
#' @examples
#' id = c('4HHB', '4FF9')
#' \donttest{
#' getSeqFromRCSBPDB(id)}

getSeqFromRCSBPDB = function (id, parallel = 5) {

  # example id : 4HHB
  # example url: https://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=fastachain&compression=NO&structureId=4hhb&chainId=A

  fastaURL = paste0('https://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=fastachain&compression=NO&structureId=', id, '&chainId=A')

  fastaTxt = getURLAsynchronous(url = fastaURL, perform = parallel)

  tmpfile = tempfile(pattern = paste0(id, '-'), fileext = '.fasta')
  for (i in 1:length(id)) write(fastaTxt[[i]], tmpfile[i])

  AASeq = lapply(tmpfile, readFASTA)

  unlink(tmpfile)

  return(AASeq)

}