R/508-extractProtCTDT.R

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

#' CTD Descriptors - Transition
#'
#' CTD Descriptors - Transition
#' 
#' This function calculates the Transition descriptor of the 
#' CTD descriptors (Dim: 21).
#' 
#' @param x A character vector, as the input protein sequence. 
#'
#' @return A length 21 named vector
#' 
#' @keywords extract CTD CTDT extrProtCTDT Transition
#'
#' @aliases extrProtCTDT
#' 
#' @author Min-feng Zhu <\email{wind2zhu@@163.com}>, 
#'         Nan Xiao <\url{http://r2s.name}>
#' 
#' @seealso See \code{\link{extrProtCTDC}} and \code{\link{extrProtCTDD}} 
#'          for Composition and Distribution of the CTD descriptors.
#' 
#' @export extrProtCTDT
#' 
#' @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 = 'BioMedR'))[[1]]
#' extrProtCTDT(x)
#' 

extrProtCTDT = 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')
    }

    # Combine single amino acids by a 2-length step

    for (i in 1:7) G[[i]] = paste(G[[i]][-n], G[[i]][-1], sep = '')
    G = lapply(G, as.factor)

    GSummary = lapply(G, summary)

    # Compute (n_rs + n_sr) / (N - 1)

    CTDT = vector('list', 7)

    for (i in 1:7) {
        CTDT[[i]][1] = sum(GSummary[[i]][c('G1G2', 'G2G1')])/(n - 1)
        CTDT[[i]][2] = sum(GSummary[[i]][c('G1G3', 'G3G1')])/(n - 1)
        CTDT[[i]][3] = sum(GSummary[[i]][c('G2G3', 'G3G2')])/(n - 1)
    }

    CTDT = unlist(CTDT)

    names(CTDT) = paste('prop', rep(1:7, each = 3), '.', 
                        rep(c('Tr1221', 'Tr1331', 'Tr2332'), times = 7) , 
                        sep = '')

    return(CTDT)

}