R/addPDBdata.R

In judyheewonlee/BCB420.2019.PDB: BCB420.2019.PDB

#' addPDBdata.R
#'
#' \code{addPDBdata} Add the PDB data retrieved from PDB. This include
#' The sequence and Resolution of each PDB chain in the database.
#'
#' Details.
#'
#' @param myDB A list. The database which is being built.
#'
#' @return myDB with the PDB data added to the database.
#'

addPDBdata <- function(myDB) {

  message("Retrieving PDB data...")
  # Call fetchPDBXML to retrieve resolutions and sequences
  # from PDB
  myPDBData <- unique(fetchPDBXML(myDB))

  # Set Resolution and sequence
  myDB$pdbChains$Resolution <- NA
  myDB$pdbChains$Sequences <- NA

  # Create a vector of the resolutions and sequences of
  # each PDB chain and add it to the DB

  sel <- match(myDB$pdbChains$ID, myPDBData$IDs)
  myDB$pdbChains$Resolution <- myPDBData[sel,]$Resolution
  myDB$pdbChains$Sequences <- myPDBData[sel,]$Sequence


  return(myDB)

}

# [END]