R/desc-07-CTDC.R

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

#' CTD Descriptors - Composition
#'
#' This function calculates the Composition descriptor of the
#' CTD descriptors (dim: 21).
#'
#' @param x A character vector, as the input protein sequence.
#'
#' @return A length 21 named vector
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @seealso See \code{\link{extractCTDT}} and \code{\link{extractCTDD}}
#' for Transition and Distribution of the CTD descriptors.
#'
#' @export extractCTDC
#'
#' @note For this descriptor type, users need to intelligently evaluate
#' the underlying details of the descriptors provided, instead of using
#' this function with their data blindly. It would be wise to use some
#' negative and positive control comparisons where relevant to help guide
#' interpretation of the results.
#'
#' @references
#' Inna Dubchak, Ilya Muchink, Stephen R. Holbrook and Sung-Hou Kim.
#' Prediction of protein folding class using global description of
#' amino acid sequence. \emph{Proceedings of the National Academy of Sciences}.
#' USA, 1995, 92, 8700-8704.
#'
#' Inna Dubchak, Ilya Muchink, Christopher Mayor, Igor Dralyuk and Sung-Hou Kim.
#' Recognition of a Protein Fold in the Context of the SCOP classification.
#' \emph{Proteins: Structure, Function and Genetics}, 1999, 35, 401-407.
#'
#' @examples
#' x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
#' extractCTDC(x)
extractCTDC <- function(x) {
  if (protcheck(x) == FALSE) {
    stop("x has unrecognized amino acid type")
  }

  group1 <- list(
    "hydrophobicity" = c("R", "K", "E", "D", "Q", "N"),
    "normwaalsvolume" = c("G", "A", "S", "T", "P", "D", "C"),
    "polarity" = c("L", "I", "F", "W", "C", "M", "V", "Y"),
    "polarizability" = c("G", "A", "S", "D", "T"),
    "charge" = c("K", "R"),
    "secondarystruct" = c("E", "A", "L", "M", "Q", "K", "R", "H"),
    "solventaccess" = c("A", "L", "F", "C", "G", "I", "V", "W")
  )

  group2 <- list(
    "hydrophobicity" = c("G", "A", "S", "T", "P", "H", "Y"),
    "normwaalsvolume" = c("N", "V", "E", "Q", "I", "L"),
    "polarity" = c("P", "A", "T", "G", "S"),
    "polarizability" = c("C", "P", "N", "V", "E", "Q", "I", "L"),
    "charge" = c(
      "A", "N", "C", "Q", "G", "H", "I", "L",
      "M", "F", "P", "S", "T", "W", "Y", "V"
    ),
    "secondarystruct" = c("V", "I", "Y", "C", "W", "F", "T"),
    "solventaccess" = c("R", "K", "Q", "E", "N", "D")
  )

  group3 <- list(
    "hydrophobicity" = c("C", "L", "V", "I", "M", "F", "W"),
    "normwaalsvolume" = c("M", "H", "K", "F", "R", "Y", "W"),
    "polarity" = c("H", "Q", "R", "K", "N", "E", "D"),
    "polarizability" = c("K", "M", "H", "F", "R", "Y", "W"),
    "charge" = c("D", "E"),
    "secondarystruct" = c("G", "N", "P", "S", "D"),
    "solventaccess" = c("M", "S", "P", "T", "H", "Y")
  )

  xSplitted <- strsplit(x, split = "")[[1]]
  n <- nchar(x)

  # Get groups for each property & each amino acid

  g1 <- lapply(group1, function(g) length(which(xSplitted %in% g)))
  names(g1) <- paste(names(g1), "Group1", sep = ".")
  g2 <- lapply(group2, function(g) length(which(xSplitted %in% g)))
  names(g2) <- paste(names(g2), "Group2", sep = ".")
  g3 <- lapply(group3, function(g) length(which(xSplitted %in% g)))
  names(g3) <- paste(names(g3), "Group3", sep = ".")
  CTDC <- unlist(c(g1, g2, g3)) / n
  # This reorders the groups from
  # p1.g1, p2.g1, p3.g1 ...
  # to
  # p1.g1, p1.g2, p1.g3 ...
  # This reordering is not really important
  # just to make the results look pretty
  ids <- unlist(lapply(1:7, function(x) x + c(0, 7, 14)))

  CTDC[ids]
}