R/split_metal_name.R

In jpquast/protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

#' Convert metal names to search pattern
#'
#' Converts a vector of metal names extracted from the \code{ft_metal} column
#' obtained with \code{fetch_uniprot} to a pattern that can be used to search for corresponding
#' ChEBI IDs. This is used as a helper function for other functions.
#'
#' @param metal_names a character vector containing names of metals and metal containing molecules.
#'
#' @return A character vector with metal name search patterns.
#' @importFrom purrr map
#' @importFrom stringr str_detect str_split str_replace_all str_extract_all str_squish
split_metal_name <- function(metal_names) {
  purrr::map_chr(metal_names, function(x) {
    if (is.na(x)) {
      result <- NA
      return(result)
    }
    # Add full name to pattern
    result <- x
    # Add split name to pattern
    # replace bracket with one whitespace
    x <- stringr::str_squish(stringr::str_replace_all(x, pattern = "[//(//)]", replacement = " "))
    if (stringr::str_detect(x, pattern = " ")) {
      x1 <- as.vector(stringr::str_split(x, pattern = " ", simplify = TRUE))
      # Remove specific words from split name
      x1 <- x1[!x1 %in% c(
        "or",
        "Divalent",
        "Monovalent",
        "metal",
        "ion",
        "Fe",
        "Cu",
        "Zn",
        "Copper",
        "a",
        "cation",
        "Iron-sulfur",
        "low-spin",
        "high-spin",
        "A",
        "A1",
        "A2",
        "A3",
        "C",
        "1",
        "1+",
        "2+",
        "2",
        "3",
        "3+",
        "4",
        "5",
        "6",
        "B",
        "b",
        "o",
        "distal",
        "axial",
        "proximal",
        "ligand",
        "heme",
        "siroheme",
        "methylcob",
        "Cob",
        "II",
        "III",
        "alamin",
        "b595",
        "b558",
        "b562",
        "b566",
        "Mo",
        "bis",
        "dinucleotide",
        "guanine",
        "Mo-bis"
      )]
      result <- append(result, x1)
    }
    # Add split "-"-containing name to pattern
    if (stringr::str_detect(x, pattern = "-")) {
      x2 <- as.vector(
        stringr::str_extract_all(x, pattern = "\\b\\w+\\-\\w+\\b", simplify = TRUE)
      )
      # Remove specific split "-"-containing names
      x2_clean <- x2[!x2 %in% c(
        "Iron-sulfur",
        "S-AdoMet",
        "Iron-oxo",
        "4Fe-2O",
        "low-spin",
        "high-spin",
        "Mo-bis",
        result
      )] # remove these names and also names that are already part of the result
      result <- append(result, x2_clean)
      x3 <-
        as.vector(stringr::str_split(
          x2,
          pattern = "-",
          simplify = TRUE
        ))
      # Remove specific words from split "-"-containing name
      x3 <- x3[!x3 %in% c(
        "sulfur",
        "4Fe",
        "4S",
        "3Fe",
        "3S",
        "2Fe",
        "2S",
        "S",
        "AdoMet",
        "oxo",
        "2O",
        "low",
        "high",
        "spin",
        "Mo",
        "bis"
      )]
      result <- append(result, x3)
    }
    result_pattern <- paste(result, collapse = "|")
    result_pattern <- str_replace(result_pattern, pattern = "\\)", replacement = "\\\\\\)")
    result_pattern <- str_replace(result_pattern, pattern = "\\(", replacement = "\\\\\\(")
    result_pattern <- str_replace(result_pattern, pattern = "\\+", replacement = "\\\\\\+")
    result_pattern
  })
}