R/gtoxCode2CASN.R

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of  ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the    ##
## GNU General Public License for more details.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# gtoxCode2CASN: Convert chemical code to CAS Registry Number
#-------------------------------------------------------------------------------

#' @title Convert chemical code to CAS Registry Number
#'
#' @description
#' \code{gtoxCode2CASN} takes a code and converts it CAS Registry Number.
#'
#' @param code Character of length 1, a chemical code
#'
#' @details
#' The function checks for the validity of the CAS Registry Number. Also,
#' the ToxCast data includes chemcials for which there is no CASRN. The
#' convention for these chemicals is to give them a CASRN as NOCAS_chid; the
#' code for these compounds is CNOCASchid. The function handles the NOCAS
#' compounds as they are stored in the database, as shown in the exmaple below.
#'
#' @examples
#' gtoxCode2CASN("C80057")
#' gtoxCode2CASN("C09812420") ## Invalid CASRN will give a warning
#' gtoxCode2CASN("CNOCAS0015") ## The underscore is reinserted for NOCAS codes
#'
#' @return A CAS Registry Number.
#'
#' @export

gtoxCode2CASN <- function(code) {

    if (length(code) > 1) {
        code <- code[1]
        warning("length of 'code' greater than 1, only the first element used.")
    }

    code <- sub("C", "", code)

    if (grepl("NOCAS", code)) {

        code <- sub("NOCAS", "NOCAS_", code)
        return(code)

    }

    if (!grepl("[a-z]|[A-Z]", code)) {

        code <- as.numeric(sapply(code, strsplit, "")[[1]])
        clen <- length(code)
        test <- sum((clen - 1):1 * code[seq_len((clen - 1))]) %% 
            10 == code[clen]
        code <- paste(
            paste(code[seq_len((clen - 3))], collapse=""),
            paste(code[(clen - 2):(clen - 1)], collapse=""),
            code[clen],
            sep="-"
        )
        if (test) return(code)
    }

    warning("'code' does not appear to have a valid CAS Registry Number.")
    code

}

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