utils_pdbProcess_.R

#' Get non-standard protein/nucleic residues
#'
#' @description
#' Get non standard protein/nucleic residues from PDB 
#'
#' @param pdb_input Pdb path 
#' 
#' @import bio3d
#' 
#' @examples 
#'
#' @export

report_nonstand <- function(pdb_input) {
  
  pdb <- tryCatch({read.pdb(pdb_input)},
                  error = function(err) {
                    return(NA)
                  })
  
  if(!is.na(pdb)) {
    #get protein 
    indx_p <- atom.select(pdb, string = "protein", inverse= TRUE)
    #get nucleic 
    indx_n <- atom.select(pdb, string = "nucleic", inverse= TRUE)
    #combine them
    indx <- combine.select(indx_p, indx_n, operator= "AND")
    #subset pdb
    clean_pdb <- trim.pdb(pdb, indx)
    nonstand <- unique(clean_pdb$atom$resid)
    return(nonstand)
  } else {
    return(NA)
  }
}


#' Process PDB file according to the selected non-standard residues
#'
#' @description
#' Process PDB file according to the selected non-standard residues
#'
#' @param pdb_input Pdb path 
#' @param nonstand_list List of non-standard residues
#' @param include_list List of non-standard residues that must be maintained in the PDB 
#' @param session
#' 
#' @import bio3d
#' @import shinyWidgets
#' 
#' @examples 
#'
#' @export
#' 

deal_sele_nonstand <- function(pdb_input, nonstand_list, include_list, session = session){
  tryCatch({ #test if the pdb_input is an appropriated PDB ID and if the read,pdb function can download successfully this pdb 
    pdb <- read.pdb(pdb_input)
    if(is.null(include_list)){
      #get nonstandard selected 
      indx_s <- atom.select(pdb, resid = nonstand_list, inverse = TRUE)
      #subset pdb
      clean_pdb <- trim.pdb(pdb, indx_s)
      #create random number to name file
      rand <- sample(x = 1:100000,size = 1)
      outfile = file.path(tempdir(), paste(rand,".pdb",sep = ""))
      #write tmp
      write.pdb(pdb = clean_pdb, file = outfile)
      return(outfile)  
    } else {
      indx_s <- atom.select(pdb, resid = nonstand_list, inverse = TRUE)
      indx_i <- atom.select(pdb, resid = include_list)
      indx <- combine.select(indx_s, indx_i, operator= "OR")
      clean_pdb <- trim.pdb(pdb, indx)
      #create random number to name file
      rand <- sample(x = 1:100000,size = 1)
      outfile = file.path(tempdir(), paste(rand,".pdb",sep = ""))
      #write tmp
      write.pdb(pdb = clean_pdb, file = outfile)
      return(outfile)  
    }
  }, error = function(e){
    shinyWidgets::sendSweetAlert(session = session,title = "Oops!", text = "Please insert a valid PDB ID.", type = "error")
  }
  )
}


#' Get only target ligand PDB 
#'
#' @description
#' Separate from protein/nucleic PDB the target ligand
#'
#' @param pdb_input Pdb path 
#' @param ligand_name Name of the ligand
#' 
#' @import bio3d
#' 
#' @examples 
#'
#' @export
#' 

get_ligand_pdb <- function(pdb_input, ligand_name){
  pdb <- read.pdb(pdb_input)
  indx_l <- atom.select(pdb, resid = ligand_name)
  clean_pdb <- trim.pdb(pdb, indx_l)
  #create random number to name file
  rand <- sample(x = 1:100000,size = 1)
  outfile = file.path(tempdir(), paste(rand,"lig.pdb",sep = ""))
  #write tmp
  write.pdb(pdb = clean_pdb, file = outfile)
  return(outfile)  
}