R/parse_adduct.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Parse adduct
#'
#' @description This function parses adducts
#'
#' @param adduct_string Adduct to be parsed
#' @param regex Regex used for parsing
#'
#' @return Parsed elements from adduct
#'
#' @export
#'
#' @examples
#' \dontrun{
#' parse_adduct("[M+H]+")
#' parse_adduct("[2M1-C6H12O6 (hexose)+NaCl+H]2+")
#' }
parse_adduct <- function(
  adduct_string,
  regex = "\\[(\\d*)M(?![a-z])(\\d*)([+-][\\w\\d].*)?.*\\](\\d*)([+-])?"
) {
  ## Full match
  matches <- stringi::stri_match_all_regex(
    str = adduct_string,
    pattern = regex
  )
  if (length(matches) > 0) {
    matches <- matches[[1]]
  } else {
    matches <- matrix(NA)
  }

  unexpected <- c(
    "n_mer" = 0,
    "n_iso" = 0,
    "los_add_clu" = 0,
    "n_charges" = 0,
    "charge" = 0
  )
  if (is.na(matches[1, 1])) {
    logger::log_warn("Invalid adduct format: {adduct_string}")
    logger::log_warn("Returning 0 instead")
    return(unexpected)
  }

  ## Extract n_mer
  n_mer <- ifelse(
    test = matches[2] != "",
    yes = matches[2] |>
      as.integer(),
    no = 1
  )

  ## Extract n_iso
  n_iso <- ifelse(
    test = matches[3] != "",
    yes = matches[3] |>
      as.integer(),
    no = 0
  )

  ## Extract modifications
  modifications <- matches[4] |>
    # Safety to allow for things like "[2M1-C6H12O6 (hexose)+NaCl+H]2+"
    gsub(pattern = " \\(.*\\)", replacement = "")

  ## Split modifications
  modifications_regex <- "[+-](\\d*)"
  modifications_elem <- stringi::stri_split_regex(
    str = modifications |>
      # Safety to allow for things like "[2M1-C6H12O6 (hexose)+NaCl+H]2+"
      gsub(pattern = " .*", replacement = ""),
    pattern = modifications_regex
  )[[1]][-1]
  modifications_sign <- stringi::stri_extract_all_regex(
    str = modifications,
    pattern = modifications_regex
  )[[1]] |>
    gsub(pattern = "\\d*", replacement = "")
  modifications_sign <- ifelse(
    test = modifications_sign == "+",
    yes = 1,
    no = -1
  )
  modifications_mult <- stringi::stri_extract_all_regex(
    str = modifications,
    pattern = modifications_regex
  )[[1]] |>
    gsub(pattern = "[+-]", replacement = "")
  modifications_mult <- ifelse(
    test = modifications_mult != "",
    yes = modifications_mult |>
      as.integer(),
    no = 1
  )

  ## Calculate mass
  modifications_masses <- modifications_elem |>
    MetaboCoreUtils::calculateMass()

  los_add_clu <- modifications_masses * modifications_mult * modifications_sign
  ## Extract n_charges
  n_charges <- ifelse(
    test = matches[5] != "",
    yes = matches[5] |>
      as.integer(),
    no = 1
  )

  ## Extract charge
  charge <- matches[6]
  charge <- ifelse(test = charge == "+", yes = 1, no = -1)

  if (
    any(
      is.na(c(
        n_mer,
        n_iso,
        los_add_clu,
        n_charges,
        charge
      )) ==
        TRUE
    )
  ) {
    logger::log_warn("Something went unexpected with the calculations")
    return(unexpected)
  } else {
    return(
      c(
        "n_mer" = n_mer,
        "n_iso" = n_iso,
        "los_add_clu" = sum(los_add_clu),
        "n_charges" = n_charges,
        "charge" = charge
      )
    )
  }
}