R/409-extractProtCTDD.R

In Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

#' CTD Descriptors - Distribution
#'
#' CTD Descriptors - Distribution
#'
#' This function calculates the Distribution descriptor of the
#' CTD descriptors (Dim: 105).
#'
#' @param x A character vector, as the input protein sequence.
#'
#' @return A length 105 named vector
#'
#' @keywords extract CTD CTDD extractProtCTDD Composition
#'
#' @aliases extractProtCTDD
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @seealso See \code{\link{extractProtCTDC}} and \code{\link{extractProtCTDT}}
#' for the Composition and Transition descriptors.
#'
#' @export extractProtCTDD
#'
#' @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 = 'Rcpi'))[[1]]
#' extractProtCTDD(x)

extractProtCTDD = function (x) {

    if (checkProt(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)

    G = vector('list', 7)
    for (i in 1:7) G[[i]] = rep(NA, n)

    # Get groups for each property & each amino acid

    for (i in 1:7) {
        try(G[[i]][which(xSplitted %in% group1[[i]])] <- 'G1')
        try(G[[i]][which(xSplitted %in% group2[[i]])] <- 'G2')
        try(G[[i]][which(xSplitted %in% group3[[i]])] <- 'G3')
    }

    # Compute Distribution

    D = vector('list', 7)
    for (i in 1:7) D[[i]] = matrix(ncol = 5, nrow = 3)

    for (i in 1:7) {
        for (j in 1:3) {
            inds = which(G[[i]] == paste0('G', j))
            quartiles = floor(length(inds) * c(0.25, 0.5, 0.75))

            quartiles[which(quartiles <= 0)] = 1

            D[[i]][j, ] = if (length(inds) > 0)
                (inds[c(1, quartiles, length(inds))]) * 100/n else 0
        }
    }

    D = do.call(rbind, D)
    D = as.vector(t(D))

    names(D) = paste(
        rep(paste('prop', 1:7, sep = ''), each = 15),
        rep(rep(c('.G1', '.G2', '.G3'), each = 5), times = 7),
        rep(paste('.residue', c('0', '25', '50', '75', '100'),
                  sep = ''), times = 21), sep = '')

    return(D)

}